Supplementary Material

CSIRO PUBLISHING www.publish.csiro.au/journals/fpb Functional Plant Biology 33, 1–24 Supplementary material:

FP05139_AC Supplementary material Molecular targets of elevated [CO2] in leaves and stems of Populus deltoides: implications for future tree growth and carbon sequestration

Nathalie DruartA,B, Marisa Rodríguez-BueyA, Greg Barron-GaffordC, Andreas SjödinA, Rishikesh BhaleraoB and Vaughan HurryA,D AUmeå Plant Science Centre, Department of Plant Physiology, Umeå University, S-901 87 Umeå, Sweden. BUmeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, S-901 83 Umeå, Sweden. CBiosphere 2 Laboratory, Columbia University, Oracle AZ 85623 USA. Current address: Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85719, USA. DCorresponding author. Email: [email protected]

Appendix S1

1.0 1.0 A B

0.5 0.5

0.0 0.0

–0.5 –0.5

–1.0 –1.0 Relative gene expression (log ) 1.0 1.0 2 C D

0.5 0.5

0.0 0.0

–0.5 –0.5 2 ) Relative gene expression (log gene expression Relative –1.0 –1.0 1.0 1.0 E F

0.5 0.5

0.0 0.0

–0.5 –0.5

–1.0 –1.0 400 800 1200 400 800 1200

Ambient [CO2] (µmol mol–1)

Validation of reproducibility of the hybridisations by comparing the hybridisation results of three genes for which two independent cDNA clones had been spotted on the array. (A, C, E leaves; B, D, F stems). (A, B) Protein phosphatase 2A, 65 kDa subunit. (C, D) Elicitor-inducible cytochrome P450. (E, F) Major storage protein.

Appendix S2. [CO2]-responsive genes in leaves sorted according to functional categories, selected up-regulated clones under 800 or –1 1200 µmol mol [CO2] Values are fold-change and those printed in bold are statistically significant with B-statistic Ն10 Function Clone ID At gene ID 800/400 1200/400 1200/800 Metabolism (01) Cytochrome P-450 PU03116 At1g13710 4.34 2.29 7.60 Cytochrome P-450 PU03121 At1g13710 4.18 2.44 8.67 Cytochrome P-450 (CYP78A9) PU05505 At3g61880 1.34 2.19 1.60 Dihydroflavonol 4-reductase PU12089 At1g61720 4.80 2.22 2.15 Naringenin 3-dioxygenase PU01480 At3g51240 –1.01 1.70 1.71 Chalcone synthase PU10149 At5g13930 1.34 1.67 1.23 Chalcone synthase PU12625 At5g13930 1.18 1.49 1.25 Chalcone synthase 1 PU04294 At5g13930 2.07 1.49 1.25 Chalcone isomerase PU04986 At3g55120 1.23 1.45 1.28 Elicitor-inducible cytochrome P450 PU08702 At1g01280 4.49 4.26 3.12 Elicitor-inducible cytochrome P450 PU12599 At5g07990 8.84 4.74 2.57 Elicitor-inducible cytochrome P450 PU12470 At5g07990 1.80 4.43 2.50 Glucosyltransferase NTGT3 PU12170 At1g07250 1.39 2.04 1.46 IPP transferase-like protein PU04004 At5g20040 –1.17 1.83 2.14 Major storage protein PU03068 At4g24340 –9.1 2.05 2.18 Major storage protein PU03117 At4g24340 –1.11 2.34 2.53 Major storage protein PU03474 At4g24340 –1.22 2.09 2.28 Major storage protein PU03508 At4g24340 –5.86 2.48 2.58 Major storage protein PU03510 At4g24340 –2.23 2.51 2.51 Major storage protein PU03513 At4g24340 –1.77 2.42 2.73 Major storage protein PU03548 At4g24340 –1.07 2.44 2.63 Major storage protein PU03698 At4g24340 –7.79 2.50 2.64 Major storage protein PU03708 At4g24340 –1.17 2.35 2.55 Major storage protein PU03743 At4g24340 –1.56 2.36 2.63 Major storage protein PU03784 At4g24340 –7.19 2.49 2.62 Major storage protein PU03820 At4g24340 –7.61 2.36 2.49 Major storage protein PU03824 At4g24340 –4.04 2.34 2.41 Major storage protein PU04029 At4g24340 –8.11 2.35 2.48 Thioredoxin H PU01940 At1g59730 1.87 1.89 1.01 Xyloglucan endotransglycosylase PU02379 At4g03210 –1.49 2.09 2.32 Xyloglucan endotransglycosylase PU07373 At4g03210 2.11 2.40 2.07 Endo-xyloglucan transferase PU11514 At5g65730 1.17 2.00 1.70 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase PU02218 At1g22410 1.06 2.21 2.28 precursor Cell growth, cell division, DNA synthesis (03) Microtubule-associated protein EB1-like protein PU03283 At5g62500 –1.08 2.52 2.72 Protein phosphatase 2A 65 kDa regulatory subunit PU05097 At3g25800 1.18 2.65 2.23 Protein phosphatase 2A 65 kDa regulatory subunit PU12228 At3g25800 1.55 3.75 2.39 Protein phosphatase 2A 65 kDa regulatory subunit PU12736 At3g25800 1.59 4.11 2.56 RGA1, giberellin response modulation protein PU03640 At2g01570 –1.11 2.20 2.44 RING zinc finger ankyrin protein-related PU03201 At2g28840 –1.12 1.85 2.08 Transcription (04) CCAAT-binding factor B subunit PU03099 At1g72830 –1.09 2.12 2.30 Probable coproporphyrinogen oxidase PU03696 At3g20740 –1.09 2.30 2.51 Protein destination (06) Peptidylprolyl isomerase PU11811 At5g48570 1.24 3.68 2.94 Ubiquitin fusion-degradation protein PU03741 At2g21270 –1.04 2.24 2.32 18.5 kDa class I heat shock protein (HSP 18.5) PU04831 At5g59720 1.28 3.77 2.93 Cell rescue, defense, cell death and ageing (11) Disease resistance response protein-related PU03542 At1g58170 –1.10 2.01 2.20 Cellular organisation (30) Pollen allergen PU06328 At4g38400 1.91 –1.21 2.32 Supplementary material Functional Plant Biology 3

Appendix S2 continued

Function Clone ID At gene ID 800/400 1200/400 1200/800 Classification not yet clear-cut (98) Expressed protein PU08410 At1g49750 1.93 1.60 –1.19 Expressed protein PU03138 At3g08780 –1.11 2.11 2.33 Expressed protein PU03140 At1g71430 –1.03 2.33 2.39 Expressed protein PU03233 At1g71080 –1.09 2.46 2.69 Expressed protein PU03245 At5g19260 –1.15 2.16 2.47 Expressed protein PU03333 At4g22920 1.05 2.29 2.17 Expressed protein PU03435 At4g01650 –1.12 2.02 2.26 Expressed protein PU03543 At4g39140 –1.07 2.13 2.28 Expressed protein PU03670 At2g21180 1.06 2.10 1.96 Expressed protein PU05874 At3g24100 1.12 2.10 1.87 Expressed protein PU06017 At4g24220 1.35 2.28 1.68 Expressed protein PU11113 At5g41080 –1.09 2.15 2.01 Expressed protein PU13336 At1g61720 2.09 2.93 2.54 Expressed protein PU07779 At5g11090 –1.31 1.76 2.32 Expressed protein PU11064 At5g41080 –7.97 2.01 Unknown protein PU03835 At1g71010 –1.07 2.09 2.22 Unclassified proteins (99) Boiling stable protein A PU00350 At3g17210 8.76 3.66 3.45 Boiling stable protein A PU01134 At3g17210 8.76 3.78 3.56 Cellulase, putative PU03243 At3g26130 –1.02 2.42 2.47 Cytochrome c oxidase polypeptide VIII PU09960 At5g23100 1.15 1.99 1.73 Expressed protein PU03457 At1g69050 –1.09 2.44 2.65 Expressed protein PU03578 At1g22420 –1.10 2.51 2.77 Expressed protein PU11117 At4g29200 1.50 –1.70 1.99 GDSL-motif lipase/hydrolase-like protein PU10319 At5g45670 2.65 1.99 9.64 GDSL-motif lipase/hydrolase-like protein PU12148 At5g45670 1.27 2.42 2.21 GDSL-motif lipase/hydrolase-like protein PU12188 At5g45670 9.55 2.49 2.33 GDSL-motif lipase/hydrolase-like protein PU12468 At5g45670 2.96 2.64 2.15 HEN1 PU12175 At4g20910 –1.06 2.18 2.30 Major storage protein PU03509 At3g17650 –1.09 2.34 2.57 Possibly polygalacturonase inhibiting protein PU08796 At5g06870 4.93 –1.20 –5.94 Polyphenol oxidase PU12604 At1g08170 3.92 2.73 –1.44 Protease inhibitor II PU03669 At2g02130 2.57 2.57 2.88 ORFs (Putative primordial protein) PU11210 At5g40260 –1.50 1.36 2.05 4 Functional Plant Biology Supplementary material

Appendix S3. [CO2]-responsive genes in leaves sorted according to functional categories, selected down-regulated clones under –1 800 or 1200 µmol mol [CO2] Values are fold-change and those printed in bold are statistically significant with B-statistic Ն10

Function Clone ID At gene ID 800/400 1200/400 1200/800 Metabolism (01) GDP-mannose pyrophosphorylase PU07331 At2g39770 –4.58 –1.79 2.55 Inositol-3-phosphate synthase PU13206 At5g10170 1.50 –1.31 –1.98 Transcription (04) DNA-binding protein, putative PU10896 At1g01060 5.90 –4.68 –2.18 DNA-binding protein, putative PU13388 At1g01060 7.60 –5.66 –2.51 Protein destination (06) DnaJ-like protein PU10218 At2g17880 –2.02 –8.67 1.46 DnaJ-like protein PU12884 At2g17880 –1.99 –7.49 2.46 DnaJ-like protein PU13066 At2g17880 –1.93 –8.53 9.26 Cell fate (14) Floricaula/leafy homolog (PTLF) PU00007 At5g61850 1.25 –2.50 –2.63 Floricaula/leafy homolog (PTLF) PU00843 At5g61850 7.42 –2.39 –2.52 Floricaula/leafy homolog (PTLF) PU03491 At5g61850 1.76 –2.14 –2.42 Floricaula/leafy homolog (PTLF) PU03680 At5g61850 1.95 –2.33 –2.37 Floricaula/leafy homolog (PTLF) PU03755 At5g61850 1.21 –2.38 –2.40 Floricaula/leafy homolog (PTLF) PU05650 At5g61850 3.41 –2.20 –2.26 Floricaula/leafy homolog (PTLF) PU12065 At5g61850 1.18 –2.62 –2.85 Floricaula/leafy homolog (PTLF) PU12438 At5g61850 3.78 –2.43 –2.50 Floricaula/leafy homolog (PTLF) PU13110 At5g61850 1.69 –2.35 –2.64 Cellular communication/signal transduction (10) Protein kinase PU13475 At2g30360 1.27 –1.54 –1.96 Cellular organisation (30) GAB3. Possibly expansin-like protein PU09319 At1g69530 –1.51 –2.06 –1.36 Classification not yet clear-cut (98) Expressed protein PU01650 At1g26800 1.26 –1.68 –2.12 Expressed protein PU08923 At1g10560 1.09 –1.97 –1.80 Unclassified proteins (99) Possibly polygalacturonase inhibiting protein PU08796 At5g06870 4.93–1.20 –5.94 Ribonucleoside-diphosphate reductase α-chain PU09892 At1g10330 –1.09 –1.80 –2.02 Supplementary material Functional Plant Biology 5

Appendix S4. [CO2]-responsive genes in stems sorted according to functional categories, selected up-regulated clones under 800 or –1 1200 µmol mol [CO2] Values are fold-change and those printed in bold are statistically significant with B-statistic Ն10 Function Clone ID At gene ID 800/400 1200/400 1200/800 Metabolism (01) Aminopeptidase like protein PU05176 At4g33090 1.97 2.09 1.06 Caffeic acid 3-O-methyltransferase PU00567 At5g54160 1.34 2.27 1.69 Caffeic acid 3-O-methyltransferase PU07978 At5g54160 1.45 2.41 1.63 Caffeoyl-CoA O-methyltransferase PU01811 At4g34050 1.41 2.07 1.47 Caffeoyl-CoA O-methyltransferase PU02461 At4g34050 1.85 2.37 1.29 Cellulose synthase PU02217 At5g44030 1.33 2.16 1.63 Cinnamyl alcohol dehydrogenase PU00508 At3g19450 1.49 2.38 1.59 Ethylene-inducible protein PU04727 At3g16050 2.23 2.70 1.21 Isoflavone reductase PU00516 At1g75280 1.24 2.52 2.03 Isoflavone reductase PU02555 At1g75280 1.43 2.30 1.61 Laccase PU02804 At2g38080 –1.17 2.10 2.46 Mitochondrial dicarboxylate carrier protein PU07562 At2g22500 1.26 2.14 1.70 Mitochondrial dicarboxylate carrier protein PU12663 At2g22500 1.50 2.35 1.56 Mitochondrial dicarboxylate carrier protein PU12705 At2g22500 1.47 2.30 1.56 Myo-inositol-1-phosphate synthase PU13206 At5g10170 1.63 2.05 1.26 PAPS-reductase-like protein precursor PU03982 At4g04610 1.55 2.67 1.72 Plastidial w-3 fatty acid desaturase PU06720 At1g07430 1.79 3.28 1.84 Protein phosphatase 2C PU12652 At2g30020 2.01 2.86 1.42 Putative basic chitinase PU01517 At3g16920 1.43 2.61 1.82 Putative basic chitinase PU06113 At3g16920 1.28 3.37 2.63 Putative polygalacturonase PG1 PU02788 At1g48100 1.92 2.11 1.10 SRC2 PU04157 At1g09070 1.65 2.02 1.22 Energy (02) Alcohol dehydrogenase 2 PU10963 At1g77120 3.06 6.16 2.01 Alcohol dehydrogenase 2 PU03309 At1g77120 1.98 2.84 1.43 Alcohol dehydrogenase 2 PU03813 At1g77120 1.87 2.48 1.33 Dicyanin PU12528 At2g32300 1.21 2.09 1.73 Heat shock protein PU05022 At5g56000 2.50 2.58 1.03 Cell growth, cell division and DNA synthesis (03) CCCH-type zinc finger protein PU10193 At2g40140 2.28 4.38 1.92 CCCH-type zinc finger protein PU03961 At2g40140 1.61 3.27 2.03 Chaperonin 60 beta-like protein PU02810 At3g13470 2.03 2.01 –1.01 DnaJ protein homolog atj3 PU05956 At3g44110 1.83 2.26 1.23 GTP-binding protein PU03770 At5g55190 2.12 2.56 1.20 GTP-binding protein PU08983 At5g55190 2.00 2.75 1.37 Heat-shock protein 80 PU02135 At5g56010 2.13 2.18 1.03 Heat-shock protein PU09805 At2g20560 1.84 2.05 1.11 Hypothetical 19.3 kDa protein PU09764 At1g01490 2.09 4.84 2.32 Hypothetical 19.3 kDa protein PU11568 At1g01490 1.27 2.23 1.76 PtxA protein precursor PU03793 At4g15160 2.09 –1.42 –2.97 SOS2-like protein kinase PKS2 PU07078 At5g58380 1.78 3.10 1.74 Transcription factor BHLH12 PU06496 At4g00480 –1.93 1.28 2.47 Transcription (04) bZip transcription factor (AtbZip60) PU13464 At1g42990 1.40 2.46 1.76 CONSTANS B-box zinc finger family protein PU08816 At3g21150 1.72 2.70 1.57 CONSTANS B-box zinc finger family protein PU10524 At3g21150 1.99 2.47 1.24 DNA-binding protein, putative PU10896 At1g01060 2.22 2.04 –1.09 DNA-binding protein, putative PU13388 At1g01060 2.57 2.35 –1.09 Ethylene responsive element binding factor 4 PU05186 At3g15210 1.82 2.15 1.18 Ethylene responsive element binding factor 4 PU07741 At3g15210 1.93 3.39 1.75 Ethylene responsive element binding factor-like protein PU13199 At4g17490 3.50 5.33 1.52 Ethylene-responsive transciptional coactivator-like protein PU03794 At3g24500 4.67 7.39 1.58 Heat shock protein PU03264 At1g74310 3.50 3.56 –1.10 High mobility group protein 2-like PU03103 At3g51880 1.29 2.64 2.05 Homeobox-leucine zipper protein ATHB-12 PU09347 At3g61890 1.30 4.15 3.19 6 Functional Plant Biology Supplementary material

Appendix S4 continued Function Clone ID At gene ID 800/400 1200/400 1200/800 Pirin-like protein PU07375 At3g59220 –1.15 1.91 2.21 SCARECROW gene regulator-like PU07055 At5g48150 1.05 2.14 2.03 Transcription factor WRKY4 PU09504 At1g80840 1.22 2.05 1.68 WRKY-type DNA binding protein PU09430 At2g46400 3.81 9.23 2.42 Protein synthesis (05) Low-molecular-weight heat shock protein-like PU05265 At5g37670 3.11 2.28 –1.36 Translation initiation factor-like protein PU05388 At5g54940 2.81 3.15 1.12 Translation initiation factor-like protein PU10245 At5g54940 2.99 3.16 1.06 Protein destination (06) Heat shock protein 70 (HSC70) PU00640 At3g12580 2.06 1.58 –1.30 Heat shock protein 70 (HSC70) PU01142 At3g12580 2.09 1.60 –1.31 Heat shock protein 70 PU06774 At3g12580 4.34 3.74 –1.16 Peptidylprolyl isomerase PU11811 At5g48570 8.00 6.75 –1.18 18.5 kDa class I heat shock protein (HSP 18.5) PU04831 At5g59720 4.84 4.05 –1.20 Cellular communication/signal transduction (10) Calcium-binding protein-like PU10452 At5g39670 1.89 4.05 2.15 Protein kinase PU13475 At2g30360 1.77 2.41 1.36 Receptor-like protein kinase PU10533 At2g31880 2.10 2.14 1.02 Regulator of gene silencing PU08510 At5g42380 3.82 5.21 1.36 Regulator of gene silencing PU12278 At5g42380 2.66 3.72 1.40 Cell rescue, defense, cell death and ageing (11) Disease resistance like protein PU00248 At5g36930 1.01 2.19 2.17 Disease resistance protein (NBS-LRR class) PU06573 At4g27220 1.20 2.76 2.30 Disease resistance protein (NBS-LRR class) PU10612 At4g27220 1.19 2.68 2.25 Hs1pro-1-like receptor PU03751 At2g40000 2.79 4.00 1.43 Pathogenesis-related protein PU04923 At4g25780 2.59 2.79 1.08 Sn-1 protein PU05856 At5g28010 –1.60 1.68 2.68 Cell fate (14) Hypothetical 39.1 kDa protein. PU03120 At3g07090 3.37 4.87 1.44 Hypothetical 39.1 kDa protein. PU12190 At3g07090 2.49 3.16 1.27 Development (25) Aquaporin PIP1-1 PU02521 At4g00430 2.03 2.36 1.16 Cellular organisation (30) Reversibly glycosylated polypeptide PU13470 At5g15650 –1.16 1.81 2.09 Classification not yet clear-cut (98) Expressed protein PU00265 At3g61490 1.80 2.23 1.24 Expressed protein PU00599 At3g57540 1.59 2.16 1.36 Expressed protein PU00607 At4g32020 1.49 2.01 1.35 Expressed protein PU00630 At1g60420 1.35 2.13 1.58 Expressed protein PU01055 At1g10560 2.22 1.27 –1.75 Expressed protein PU01369 At3g61490 2.03 2.43 1.19 Expressed protein PU01908 At1g09310 1.72 2.00 1.16 Expressed protein PU02796 At3g01680 1.71 2.44 1.43 Expressed protein PU03447 At2g15960 –3.25 –1.63 2.00 Expressed protein PU03458 At4g24220 –1.32 1.60 2.11 Expressed protein PU03484 At5g42050 1.54 2.34 1.51 Expressed protein PU04714 At5g51190 1.56 3.23 2.07 Expressed protein PU04936 At3g01680 1.79 3.02 1.68 Expressed protein PU05076 At1g32700 1.45 2.00 1.38 Expressed protein PU05525 At3g01680 1.40 2.26 1.61 Expressed protein PU05813 At5g51190 1.90 3.66 1.93 Expressed protein PU05874 At3g24100 3.28 3.37 1.03 Expressed protein PU06343 At5g42050 1.79 3.00 1.67 Expressed protein PU06842 At5g38070 2.06 1.12 –1.85 Expressed protein PU07391 At1g09750 2.27 1.34 –1.70 Expressed protein PU08533 At3g21570 1.35 2.23 1.65 Expressed protein PU08876 At5g11090 1.97 3.00 1.52 Expressed protein PU08923 At1g10560 3.94 6.01 1.53 Supplementary material Functional Plant Biology 7

Appendix S4 continued Function Clone ID At gene ID 800/400 1200/400 1200/800 Expressed protein PU09113 At5g11090 2.74 3.05 1.11 Expressed protein PU09474 At1g60420 –1.09 2.04 2.24 Expressed protein PU09971 At1g60420 1.35 2.12 1.56 Expressed protein PU10173 At5g17350 1.31 2.30 1.76 Expressed protein PU10597 At3g07600 1.72 4.51 2.62 Expressed protein PU10629 At1g05575 1.56 2.90 1.86 Expressed protein PU11800 At1g59710 1.72 2.75 1.60 Expressed protein PU12036 At5g42050 1.92 3.20 1.67 Expressed protein PU12149 At4g27280 1.20 2.19 1.83 Similar to senescence-associated protein PU08184 At2g23810 1.58 2.30 1.45 Similar to senescence-associated protein PU12080 At2g23810 1.80 2.42 1.34 Unclassified proteins (99) Ankyrin-repeat protein HBP1 PU04347 At2g17390 2.22 2.37 1.07 CMP-N-acetylneuraminate-beta-galactosamide- PU09672 At5g05650 4.04 1.19 1.21 alpha-2,3-sialyltransferase ORF YLL020C. PU02350 At1g02816 2.22 2.15 –1.03 Expressed protein PU04190 At5g48250 1.25 2.06 1.66 Expressed protein PU09267 At3g61710 –1.10 2.10 2.31 Expressed protein PU10116 At1g30260 2.08 4.90 2.36 Expressed protein PU10334 At1g72650 1.47 2.11 1.44 Expressed protein PU10429 At5g67250 1.96 2.70 1.38 Non-specific lipid transfer-like protein PU00488 At5g48490 2.18 1.76 –1.23 Non-specific lipid transfer-like protein PU01768 At5g48490 2.69 2.00 –1.35 Non-specific lipid transfer-like protein PU02501 At5g48490 2.24 1.68 –1.33 Ubiquitin-like protein PU09006 At5g42300 2.01 2.86 1.43 8 Functional Plant Biology Supplementary material

Appendix S5. [CO2]-responsive genes in stems sorted according to functional categories, selected down-regulated clones under –1 800 or 1200 µmol mol [CO2] Values are fold-change and those printed in bold are statistically significant with B-statistic Ն10 Function Clone ID At gene ID 800/400 1200/400 1200/800 Metabolism (01) Chalcone-flavonone isomerase PU04986 At3g55120 –1.52 –2.07 –1.45 Chalcone synthase 1 PU04294 At5g13930 –2.11 –2.81 –1.33 Chalcone synthase PU10149 At5g13930 –1.50 –3.12 –2.08 Chalcone synthase PU12625 At5g13930 –1.35 –4.03 –2.99 Dihydroflavonol 4-reductase PU12089 At5g42800 –1.59 –4.23 –2.66 Dihydroflavonol 4-reductase PU12348 At5g42800 –1.17 –2.29 –1.95 Elicitor-inducible cytochrome P450 PU08702 At1g01280 1.06 –1.98 –2.10 Elicitor-inducible cytochrome P450 PU12470 At1g01280 –1.14 –2.13 –1.87 Flavanone 3-hydroxylase (FH3) PU01480 At3g51240 –1.48 –3.16 –2.14 Flavonoid 3-hydroxylase PU11503 At5g07990 –1.45 –2.40 –1.65 Flavonoid 3-hydroxylase PU12061 At5g07990 –1.53 –2.75 –1.80 GDP-mannose pyrophosphorylase PU03161 At2g39770 –1.36 –2.25 –1.66 Glucosyltransferase NTGT3 PU12170 At1g07250 –1.33 –2.28 –1.71 Leucoanthocyanidin dioxygenase (LDOX) PU12098 At4g22880 –1.66 –3.51 –2.12 Leucoanthocyanidin dioxygenase (LDOX) PU12918 At4g22880 –1.66 –3.44 –2.07 Pectinesterase-like protein PU01896 At3g49220 –1.17 –2.40 –2.06 Phenylcoumaran benzylic ether reductase homolog PU08497 At1g75290 –1.60 –2.72 –1.70 Seed imbibition protein PU01324 At3g57520 1.56 –1.32 –2.05 Thioredoxin H PU11831 At1g59730 –1.45 –2.01 –1.39 Xyloglucan endotransglycosylase PU02379 At4g03210 –2.30 –2.00 1.15 Xyloglucan endotransglycosylase PU05203 At4g03210 –2.16 –2.40 –1.11 Xyloglucan endotransglycosylase PU07448 At4g03210 –2.52 –1.96 1.29 Cell growth, cell division and DNA synthesis (03) Protein phosphatase 2A 65 kDa regulatory subunit PU12228 At3g25800 1.01 –2.04 –2.06 Protein phosphatase 2A 65 kDa regulatory subunit PU12736 At3g25800 1.04 –1.92 –2.00 PtxA protein precursor PU03692 At4g15160 1.98 –1.36 –2.69 PtxA protein precursor PU03793 At4g15160 2.09 –1.42 –2.97 PtxA protein precursor PU12497 At4g15160 1.62 –1.23 –2.00 Protein destination (06) Calcium sensor homolog PU04805 At5g24270 –1.82 –2.60 –1.43 Protein transport protein SEC61 gamma subunit PU05824 At4g24920 –1.80 –2.50 –1.39 Cell rescue, defense, cell death and ageing (11) Peroxidase PU01171 At2g22420 –1.55 –2.35 –1.51 Cellular organisation (30) Pollen allergen PU01133 At4g38400 –2.09 –2.42 –1.16 Pollen allergen PU06328 At4g38400 –3.66 –2.80 1.31 Possibly expansin-like protein PU05915 At1g69530 1.97 –1.14 –2.24 Classification not yet clear-cut (98) Expressed protein PU00022 At3g15430 –2.29 –2.20 1.04 Expressed protein PU00768 At3g15430 –2.47 –2.14 1.15 Expressed protein PU01431 At3g15430 –2.43 –2.04 1.19 Expressed protein PU01755 At3g15430 –2.24 –2.23 1.01 Expressed protein PU02181 At4g37300 –2.50 –2.53 –1.01 Expressed protein PU02241 At5g51550 –1.05 –2.09 –2.00 Expressed protein PU02279 At3g15430 –2.20 –2.35 –1.07 Expressed protein PU03447 At2g15960 –3.25 –1.63 1.99 Expressed protein PU05109 At5g51550 –1.15 –2.02 –1.76 Expressed protein PU06567 At1g78060 1.52 –1.51 –2.30 Expressed protein PU06812 At5g51550 –1.09 –2.12 –1.95 Expressed protein PU07693 At2g17230 –2.40 –2.44 –1.02 Expressed protein PU07716 At3g15430 –2.38 –1.96 1.22 Expressed protein PU07779 At5g11090 –1.62 –2.10 –1.29 Expressed protein PU08808 At5g05270 –1.79 –3.22 –1.80 Expressed protein PU08856 At5g05270 –1.69 –3.41 –2.02 Expressed protein PU12444 At2g15960 –2.55 –1.63 1.57 Supplementary material Functional Plant Biology 9

Appendix S5 continued Function Clone ID At gene ID 800/400 1200/400 1200/800 Expressed protein PU12229 At1g05350 1.40 –1.83 –2.56 Expressed protein PU13336 At1g61720 –1.62 –3.02 –1.87 Expressed protein PU13400 At3g08030 1.40 –1.74 –2.44 Pseudo-response regulator 5 (APRR5) PU00695 At5g24470 –2.29 –1.61 1.42 Unclassified proteins (99) Boiling stable protein A PU00350 At3g17210 –1.54 –2.08 –1.35 Boiling stable protein A PU01134 At3g17210 –1.43 –2.08 –1.46 Conserved hypothetical protein PU00175 At1g34650 –1.61 –2.54 –1.58 GDSL-motif lipase/hydrolase-like protein PU12468 At5g45670 1.48 –1.63 –2.40 Hypothetical protein yncM PU05373 At5g35650 –1.48 –2.40 –1.62 Populus x generosa pop3 peptide PU05523 At3g17210 –2.00 –2.70 –1.36 Populus x generosa pop3 peptide PU12666 At3g17210 –1.81 –2.93 –1.62 Possibly glycine-rich RNA binding protein PU02308 At2g21660 –2.13 –2.01 1.06 Proline-rich cell wall protein PU08800 At2g14890 –1.35 –2.17 –1.60 Wound-induced protein PU05421 At4g10270 –1.70 –2.08 –1.22 10 Functional Plant Biology Supplementary material

Appendix S6. Effect of long-term stable increases in [CO2] on the expression profile of energy-related genes in leaf and stem tissue Relative expression refers to fold changes between the two samples. Values printed in bold are statistically significant with B-statistic Ն10 Relative expression Leaves Stems Function Clone ID Gene ID 800/400 1200/400 1200/800 800/400 1200/400 1200/800 Energy GTP-binding protein PU03856 At1g02280 –1.15 –1.19 –1.04 –1.11 –1.21 –1.09 GTP-binding protein PU07129 At1g02280 –1.02 1.01 1.03 –1.09 –1.13 –1.03 Cytochrome b-561, putative PU03011 At1g26100 1.14 –0.96 –1.10 1.07 1.36 1.27 Nodulin-like protein PU03199 At1g80530 –1.08 0.95 1.03 –1.06 –1.03 1.02 Nodulin-like protein PU05979 At1g80530 1.02 1.12 1.10 1.03 –1.06 –1.10 NADH dehydrogenase subunit 6 (EC 1.6.5.3) PU10445 At2g29990 –1.14 –1.15 –1.01 1.09 1.14 1.05 NADH dehydrogenase subunit 6 (EC 1.6.5.3) PU10493 At2g29990 –1.30 –1.43 –1.10 –1.41 –1.03 1.36 Expressed protein PU01329 At2g38710 –1.05 –1.19 –1.13 1.07 –1.04 –1.11 Expressed protein PU02141 At2g38710 1.03 0.98 –1.05 –1.46 –1.79 –1.22 Expressed protein PU07776 At2g38710 1.07 –0.98 –1.05 1.14 1.13 1.00 Expressed protein PU09022 At3g13200 0.93 1.01 1.09 –1.02 1.00 1.02 Copper chaperone COX17-1 PU01971 At3g15352 –1.15 –1.02 1.13 –1.30 1.01 1.32 Heat shock transcription factor 29 PU06279 At3g15352 –1.03 –1.83 –1.77 1.48 1.83 1.23 Expressed protein PU06918 At3g59650 -1.06 1.03 1.09 –1.03 –1.14 –1.10 NADH dehydrogenase PU00242 At4g05020 1.00 1.00 –1.01 –1.49 –1.01 1.47 NADH dehydrogenase PU06352 At4g05020 1.01 1.05 1.04 –1.21 –1.40 –1.16 NADH dehydrogenase PU12467 At4g05020 1.08 1.11 1.02 1.16 –1.15 –1.34 NADH dehydrogenase PU13025 At4g05020 1.05 –1.01 –1.06 –1.08 –1.15 0.94 Expressed protein PU03072 At4g25570 –1.11 –1.04 1.07 –1.14 –1.14 1.00 Cytochrome PU05666 At4g25570 –1.04 1.06 1.11 1.19 1.29 1.08 Expressed protein PU08772 At4g30480 1.03 1.09 1.06 1.32 1.20 –1.10 Expressed protein PU11656 At4g30480 –1.04 –1.02 1.02 1.17 1.44 1.23 Expressed protein PU01515 At4g37830 1.06 –1.04 –1.10 1.04 –1.08 –1.12 Cytochrome b-561 PU04189 At5g38630 –1.05 –1.00 1.05 –1.06 –1.23 –1.16 NADH dehydrogenase 10.5K chain-like PU07349 At5g47890 –1.06 –1.07 1.00 1.04 –1.18 –1.23 protein NADH dehydrogenase 10.5K chain-like PU11338 At5g47890 –1.07 –1.02 1.05 –2.43 –1.05 2.31 protein Electron transport Expressed protein PU03523 At1g02890 –1.10 –1.02 1.08 –1.15 1.02 1.17 Expressed protein PU07912 At1g02890 1.04 1.05 1.01 1.03 1.11 1.08 Expressed protein PU05615 At1g02890 –1.06 –1.01 1.05 –1.07 1.00 1.07 Expressed protein PU09034 At1g07180 1.12 –1.11 –1.25 –1.16 1.04 1.21 Ascorbate peroxidase PU00482 At1g07890 1.13 1.06 –1.07 1.20 1.03 –1.16 Expressed protein PU04224 At1g07960 1.24 –1.12 –1.39 1.15 1.38 1.19 Thioredoxin PU11159 At1g08570 –1.58 –1.92 –1.22 1.54 1.80 1.17 Thioredoxin PU09808 At1g08570 –1.51 –1.75 –1.16 1.41 1.52 1.07 Ferredoxin-like protein PU11735 At1g10960 1.07 –1.05 –1.12 1.25 1.64 1.31 Ferredoxin-like protein PU08371 At1g10960 1.03 –1.08 –1.11 –1.06 –1.24 –1.17 Mandelonitrile lyase PU11698 At1g14190 –1.03 –1.04 –1.01 –1.17 1.08 1.27 Thioredoxin, putative PU13348 At1g15020 1.12 1.16 1.03 –1.19 –1.11 1.07 Expressed protein PU07348 At1g17130 –1.21 –1.10 1.10 –1.24 1.10 1.37 Expressed protein PU00596 At1g17130 –1.02 –1.03 –1.02 –1.12 –1.21 –1.09 Plastocyanin B, chloroplast precursor PU06425 At1g20340 1.02 1.05 1.03 1.46 1.35 –1.08 Protein disulfide isomerase precursor (PDI) PU07520 At1g21750 –1.02 1.06 1.08 –1.27 –1.23 1.04 (EC 5.3.4.1) Protein disulfide isomerase precursor (PDI) PU06743 At1g21750 –1.03 1.06 1.09 –1.21 –1.18 1.02 (EC 5.3.4.1) Protein disulfide isomerase precursor (PDI) PU06399 At1g21750 1.01 1.12 1.10 –1.18 –1.17 1.01 (EC 5.3.4.1) Protein disulfide isomerase precursor (PDI) PU03931 At1g21750 –1.04 1.16 1.20 –1.22 –1.21 1.00 (EC 5.3.4.1) Protein disulfide isomerase precursor (PDI) PU07569 At1g21750 –1.04 1.05 1.09 –1.17 –1.24 –1.06 (EC 5.3.4.1) Supplementary material Functional Plant Biology 11

Appendix S6 continued Relative expression Leaves Stems Function Clone ID Gene ID 800/400 1200/400 1200/800 800/400 1200/400 1200/800 Subunit 6b of cytochrome c oxidase PU05707 At1g22450 –1.04 –1.05 –1.02 1.10 1.24 1.12 POSSIBLY Subunit 6b of cytochrome c PU06811 At1g22450 –1.03 –1.05 –1.02 –1.13 –1.02 1.11 oxidase Subunit 6b of cytochrome c oxidase PU09162 At1g22450 1.05 1.03 –1.02 –1.12 –1.15 –1.03 Subunit 6b of cytochrome c oxidase PU07566 At1g22450 1.03 –1.09 –1.12 1.13 1.01 –1.12 Subunit 6b of cytochrome c oxidase PU04711 At1g22450 1.00 1.16 1.15 1.02 –1.10 –1.12 Superoxide-generating NADPH oxidase PU00451 At1g23020 –1.12 –1.18 –1.06 –1.04 1.55 1.60 flavocytochrome Thylakoid structural protein PU08928 At1g23040 1.02 –1.03 –1.05 –1.13 1.01 1.15 Expressed protein PU01489 At1g25682 –1.08 –1.05 1.03 –1.38 –1.63 –1.18 Unknown protein (At1g34780; F21H2.1) PU07900 At1g34780 –1.05 1.01 1.06 –1.32 1.23 1.62 Unknown protein (At1g34780; F21H2.1) PU03267 At1g34780 –1.03 1.07 1.11 –1.05 –1.12 –1.06 Protein disulfide isomerase, putative PU04229 At1g35620 –1.07 –1.05 1.03 1.03 –1.23 –1.27 (At1g35620) Hypothetical protein, 5 partial PU06485 At1g50140 –1.02 1.05 1.07 –1.25 –1.18 1.06 Thioredoxin like protein PU09242 At1g50320 –1.06 –1.25 –1.18 –1.13 1.04 1.17 Electron transport flavo protein-related PU06854 At1g50940 1.00 1.04 1.04 –1.11 –1.00 1.10 ATP synthase epsilon chain, mitochondrial PU06522 At1g51650 1.02 1.01 –1.01 1.04 1.01 –1.04 (EC 3.6.3.14) ATP synthase epsilon chain, mitochondrial PU00785 At1g51650 1.03 –1.01 –1.04 1.20 –1.12 –1.34 (EC 3.6.3.14) Protein disulfide isomerase precursor, putative PU06713 At1g52260 1.04 –1.01 –1.05 –1.04 1.09 1.14 Expressed protein PU09474 At1g60420 –1.26 –1.36 –1.08 –1.09 2.04 2.24 Expressed protein PU00630 At1g60420 1.06 1.33 1.25 1.35 2.13 1.58 Expressed protein PU09971 At1g60420 –1.05 1.18 1.24 1.35 2.12 1.56 Expressed protein PU08865 At1g60420 1.04 –1.22 –1.27 –1.07 1.09 1.17 Expressed protein PU04090 At1g60420 –1.09 –1.02 1.07 1.04 –1.04 –1.08 Blue copper protein precursor PU00078 At1g72230 1.25 –1.05 –1.31 1.39 2.41 1.74 Blue copper protein precursor PU00221 At1g72230 1.03 1.01 –1.02 1.24 1.83 1.47 Blue copper protein precursor PU06349 At1g72230 1.35 1.17 –1.16 1.07 1.40 1.31 Blue copper protein precursor PU01792 At1g72230 1.11 1.09 –1.01 1.02 1.29 1.26 Blue copper protein precursor PU01814 At1g72230 1.17 1.10 –1.06 1.31 1.63 1.24 Blue copper protein precursor PU01766 At1g72230 1.08 1.06 –1.02 –1.28 –1.04 1.24 Blue copper protein precursor PU07720 At1g72230 1.31 1.13 –1.16 1.37 1.66 1.22 Blue copper protein precursor PU02148 At1g72230 1.11 1.04 –1.07 1.69 1.65 –1.03 Expressed protein PU12038 At1g72970 1.02 1.03 1.01 –1.18 1.45 1.72 Alcohol dehydrogenase 2 (EC 1.1.1.1) PU10963 At1g77120 1.22 –1.60 –1.95 3.06 6.16 2.01 Alcohol dehydrogenase 2 (EC 1.1.1.1) PU03309 At1g77120 1.29 –1.48 –1.90 1.98 2.84 1.43 Alcohol dehydrogenase 2 (EC 1.1.1.1) PU03813 At1g77120 1.31 –1.47 –1.92 1.87 2.48 1.33 Alcohol dehydrogenase 2 (EC 1.1.1.1) PU03141 At1g77120 1.31 1.08 –1.21 –1.40 –1.12 1.25 Alcohol dehydrogenase 2 (EC 1.1.1.1) PU04010 At1g77120 1.14 1.32 1.16 1.49 1.34 –1.12 Alcohol dehydrogenase 2 (EC 1.1.1.1) PU00686 At1g77120 1.07 1.19 1.12 1.41 1.18 –1.19 Cytochrome c oxidase subunit-related PU00816 At1g80230 1.04 1.02 –1.02 –1.05 –1.15 –1.10 Cytochrome c oxidase subunit-related PU09005 At1g80230 –1.00 –1.04 –1.04 –1.07 –1.31 –1.22 Expressed protein PU04246 At2g01270 –1.02 1.11 1.13 1.03 1.20 1.17 Expressed protein PU13431 At2g01270 –1.10 1.01 1.11 –1.09 –1.06 1.03 Expressed protein PU11983 At2g01270 1.04 1.00 –1.03 –1.29 –1.30 –1.01 Expressed protein PU12007 At2g01270 –1.07 1.03 1.10 1.11 1.10 –1.01 Ferredoxin-thioredoxin reductase PU03626 At2g04700 –1.03 –1.10 –1.06 1.05 1.05 1.00 AAA-type ATPase PU07903 At2g18190 1.03 1.05 1.01 –1.05 1.10 1.16 AAA-type ATPase PU08086 At2g18190 1.17 1.07 –1.09 1.55 1.22 –1.27 ATP binding protein PU02621 At2g18990 1.11 1.06 –1.04 –1.04 –1.03 1.01 ATP binding protein PU03028 At2g18990 1.16 1.16 –1.00 1.07 1.00 –1.07 Expressed protein PU02323 At2g25950 –1.06 1.16 1.22 –1.16 1.01 1.17 Expressed protein PU12566 At2g26070 –1.01 –1.06 –1.05 –1.33 1.28 1.70 Post-floral-specific protein (PPF-1 protein) PU10280 At2g28800 –1.14 –1.18 –1.04 1.11 1.18 1.06 12 Functional Plant Biology Supplementary material

Appendix S6 continued Relative expression Leaves Stems Function Clone ID Gene ID 800/400 1200/400 1200/800 800/400 1200/400 1200/800 Dicyanin PU12528 At2g32300 1.06 1.21 1.13 1.21 2.09 1.73 Dicyanin PU08771 At2g32300 1.13 –1.17 –1.32 –1.20 1.28 1.54 ATP synthase gamma chain, mitochondrial PU08227 At2g33040 1.06 1.05 –1.01 1.04 1.17 1.13 precursor (EC 3.6.3.14) ATP synthase gamma chain, mitochondrial PU00245 At2g33040 1.10 –1.02 –1.12 1.10 1.21 1.09 precursor (EC 3.6.3.14) ATP synthase gamma chain, mitochondrial PU07178 At2g33040 1.07 1.07 –1.00 1.09 –1.23 –1.34 precursor (EC 3.6.3.14) Expressed protein PU01082 At2g35760 1.02 1.12 1.09 1.00 –1.00 –1.01 Expressed protein PU13187 At2g38000 –1.30 –1.40 –1.08 –1.30 –1.14 1.14 Expressed protein PU08168 At2g38270 –1.08 1.05 1.14 –1.08 –1.00 1.08 Expressed protein PU09202 At2g46620 –1.12 –1.06 1.06 –1.09 1.10 1.20 Cytochrome c oxidase subunit 5c PU03822 At2g47380 –1.01 1.11 1.12 1.00 1.07 1.06 Cytochrome c oxidase subunit 5c PU13166 At2g47380 1.02 1.03 1.01 –1.04 –1.32 –1.27 Protein disulfide-isomerase PU01124 At2g47470 –1.10 –1.23 –1.12 –1.08 1.33 1.43 Protein disulfide-isomerase PU03843 At2g47470 –1.24 –1.19 1.04 –1.23 –1.38 –1.12 Protein disulfide-isomerase PU00220 At2g47470 1.08 1.16 1.08 1.13 –1.07 –1.21 Protein disulfide-isomerase PU00748 At2g47470 1.05 1.12 1.06 1.13 –1.12 –1.27 AAA ATPase PU04682 At3g01610 –1.00 –1.05 –1.05 –1.09 –1.12 –1.03 Thioredoxin F-type, chloroplast precursor PU10314 At3g02730 1.03 –1.00 –1.04 1.18 1.05 –1.12 (TRX-F) Expressed protein PU04016 At3g03100 1.09 1.08 –1.01 –1.36 –1.50 –1.10 Expressed protein PU04675 At3g04340 1.03 –1.06 –1.09 –1.08 –1.13 –1.05 Expressed protein PU02721 At3g04780 1.01 –1.01 –1.03 –1.21 –1.19 1.02 Expressed protein PU07387 At3g04780 1.11 1.03 –1.07 1.47 1.36 –1.08 Phytochrome B2 PU12031 At3g06310 1.03 –1.06 –1.09 –1.02 –1.12 –1.11 Expressed protein PU09291 At3g06390 1.05 –1.23 –1.28 –1.19 1.04 1.24 Thioredoxin-like protein PU03807 At3g08710 –1.14 1.01 1.15 –1.18 1.05 1.24 Ascorbate peroxidase 2 PU02971 At3g09640 –1.20 1.06 1.27 –1.07 1.17 1.25 Ascorbate peroxidase 3 PU06690 At3g09640 1.18 1.20 1.02 1.14 1.08 –1.05 Expressed protein PU09520 At3g12260 –1.02 –1.04 –1.02 1.13 1.36 1.20 Expressed protein PU07694 At3g12260 1.09 1.04 –1.05 –1.06 –1.06 1.00 Expressed protein PU02427 At3g12260 1.03 –1.06 –1.09 –1.13 –1.14 –1.01 Expressed protein PU12169 At3g12260 –1.26 –1.04 1.21 –1.02 –1.07 –1.05 Hypothetical protein PU02278 At3g15140 1.01 1.00 1.07 1.15 1.58 1.37 Hypothetical protein PU12294 At3g15140 1.05 1.03 –1.02 –1.30 –1.22 1.06 Hypothetical protein PU00118 At3g15140 –1.07 1.03 1.10 –1.19 –1.20 –1.01 Thioredoxin M-type, chloroplast precursor PU09582 At3g15360 –1.04 –1.10 –1.05 1.07 1.32 1.23 (TRX-M) Thioredoxin m2 PU02636 At3g15360 –1.25 –1.06 1.18 1.05 1.25 1.20 Thioredoxin M-type, chloroplast precursor PU10123 At3g15360 –1.01 –1.04 –1.03 –1.32 –1.13 1.16 (TRX-M) Glutathione reductase, cytosolic (EC 1.8.1.7) PU05036 At3g24170 1.10 1.13 1.03 –1.16 1.04 1.20 Glutathione reductase, cytosolic PU09132 At3g24170 1.08 1.05 –1.03 –1.10 –1.10 –1.00 MRP protein (ATP/GTP-binding protein) PU08754 At3g24430 1.15 –1.07 –1.24 1.20 1.14 –1.06 Rubisco expression protein-related PU05851 At3g24530 –1.05 1.08 1.14 –1.28 –1.06 1.21 Rubisco expression protein-related PU07539 At3g24530 –1.12 1.15 1.29 1.13 1.29 1.14 Expressed protein PU01533 At3g24730 1.03 1.03 1.00 1.07 –1.07 –1.15 Blue copper protein, putative PU00311 At3g27200 –1.06 –1.02 1.03 –1.04 1.26 1.31 NADPH:quinone oxidoreductase (NQR) PU02208 At3g27890 1.22 1.22 1.00 –1.25 –1.22 1.02 Expressed protein PU05692 At3g28540 1.07 1.03 –1.04 –1.21 –1.18 1.02 Expressed protein PU02639 At3g44370 –1.01 –1.07 –1.06 –1.22 –1.18 1.03 Expressed protein PU08438 At3g48200 –1.16 –1.35 –1.16 –1.08 1.02 1.10 Thioredoxin H PU08713 At3g51030 1.06 –1.00 –1.06 1.05 1.24 1.18 Thioredoxin H PU01266 At3g51030 1.09 1.04 –1.06 1.28 1.36 1.06 Thioredoxin H PU02305 At3g51030 1.00 1.02 1.01 1.32 1.31 –1.01 Supplementary material Functional Plant Biology 13

Appendix S6 continued Relative expression Leaves Stems Function Clone ID Gene ID 800/400 1200/400 1200/800 800/400 1200/400 1200/800 Expressed protein PU04399 At3g51040 –1.14 –1.10 1.04 1.25 1.12 –1.11 Expressed protein PU00636 At3g51040 1.03 1.05 1.02 –1.07 –1.39 –1.30 Cell division cycle protein 48 homolog PU06260 At3g53230 1.10 –1.06 –1.16 1.02 1.01 –1.01 Cell division cycle protein 48 homolog PU08037 At3g53230 1.11 –1.03 –1.14 1.06 1.02 –1.03 Cell division cycle protein 48 homolog PU01047 At3g53230 1.09 –1.02 –1.11 1.19 –1.03 –1.23 Cell division cycle protein 48 homolog PU00805 At3g53230 1.11 –1.06 –1.18 1.12 –1.13 –1.26 Expressed protein PU07658 At3g54900 –1.08 –1.08 –1.01 1.09 1.26 1.16 Protein disulfide-isomerase-like protein PU06421 At3g54960 1.14 –1.02 –1.16 –1.11 1.64 1.83 Protein disulfide-isomerase-like protein PU04109 At3g54960 1.15 –1.08 –1.23 –1.01 1.45 1.47 Protein disulfide-isomerase-like protein PU11184 At3g54960 1.13 –1.04 –1.18 1.06 1.39 1.31 Protein disulfide-isomerase-like protein PU11662 At3g54960 1.18 1.05 –1.12 –1.02 –1.17 –1.14 Quinone reductase-like protein PU09353 At3g56460 1.05 –1.17 –1.23 1.01 1.42 1.41 Quinone reductase-like protein PU04749 At3g56460 1.03 –1.10 –1.13 –1.91 –1.80 1.06 Uclacyanin 3 PU00579 At3g60280 1.03 –1.13 –1.16 1.12 –1.00 –1.13 Uclacyanin 3 PU09517 At3g60280 –1.12 –1.22 –1.08 –1.15 –1.52 –1.32 Uclacyanin 3-like protein PU07655 At3g60280 –1.04 –1.03 1.01 1.55 1.12 –1.38 ATP synthase gamma chain, chloroplast PU11720 At4g04640 –1.08 –1.16 –1.07 1.04 1.44 1.38 precursor (EC 3.6.3.14) N-ethylmaleimide sensitive fusion protein PU10622 At4g04910 –1.08 –1.04 1.04 –1.06 –1.07 –1.01 Thioredoxin PU04768 At4g04950 1.23 –1.08 –1.32 –1.06 1.04 1.11 Thioredoxin PU11601 At4g04950 1.07 –1.02 –1.09 1.01 1.08 1.07 Oxygen-evolving enhancer protein 3, PU09326 At4g05180 –1.08 1.00 1.08 –1.02 1.21 1.23 chloroplast Oxygen-evolving enhancer protein 3, PU08604 At4g05180 –1.07 –1.04 1.03 1.29 1.19 –1.08 chloroplast Ferredoxin–NADP reductase, root isozyme, PU09707 At4g05390 –1.14 1.06 1.20 –1.01 –1.01 –1.00 chloroplast precursor(EC 1.18.1.2) Ferredoxin–NADP reductase, root isozyme, PU11991 At4g05390 –1.07 1.14 1.22 –1.06 –1.15 –1.09 chloroplast precursor(EC 1.18.1.2) Blue copper-binding protein, 15K (lamin) PU02010 At4g12880 1.07 1.11 1.04 –1.20 –1.13 1.07 Ferredoxin PU10882 At4g14890 1.07 1.00 –1.07 –1.03 1.19 1.23 ATP binding protein-like PU06010 At4g19540 –1.00 –1.00 1.00 –1.11 –1.14 –1.03 ATP binding protein-like PU11721 At4g19540 1.00 1.05 1.04 1.74 1.19 –1.47 Expressed protein PU02280 At4g25650 –1.01 –1.29 –1.27 1.06 1.25 1.18 Zinc-finger protein zfs1 PU04450 At4g25650 –1.13 –1.04 1.09 1.29 1.36 1.05 Hypothetical 10.4 kDa protein PU11317 At4g25650 –1.16 –1.16 –1.00 –1.19 –1.24 –1.04 Expressed protein PU06126 At4g25650 –1.06 –1.19 –1.12 1.02 –1.24 –1.27 Expressed protein PU02475 At4g27680 1.02 –1.07 –1.08 –1.03 –1.22 –1.18 Thioredoxin-like protein PU05816 At4g29670 –1.10 –1.14 –1.03 –1.20 –1.08 1.11 Expressed protein PU05086 At4g29720 –1.01 1.24 1.26 –1.14 –1.02 1.11 Thiol-disulfide interchange like protein PU10918 At4g37200 –1.10 –1.21 –1.10 –1.18 –1.07 1.11 Thiol-disulfide interchange like protein PU08989 At4g37200 –1.11 –1.19 –1.07 –1.08 –1.01 1.07 Hypothetical membrane-spanning protein PU11785 At5g06430 –1.14 1.07 1.22 1.09 1.09 1.00 FN0587 Expressed protein PU02378 At5g08290 –1.01 1.18 1.19 –1.05 1.06 1.11 Expressed protein PU12251 At5g08290 –1.08 1.15 1.24 1.07 1.12 1.05 Ubiquinol-cytochrome C reductase iron-sulfur PU02083 At5g13430 1.05 1.03 –1.03 –1.06 1.06 1.12 subunit 2, mitochondrial precursor (EC 1.10.2.2) Ubiquinol-cytochrome C reductase iron-sulfur PU01640 At5g13430 1.05 1.01 –1.04 –1.05 –1.26 –1.20 subunit 2, mitochondrial precursor (EC 1.10.2.2) Expressed protein PU01070 At5g14240 1.06 1.07 1.01 –1.10 –1.13 –1.03 Ubiquinol-cytochrome C reductase complex PU10802 At5g15350 –1.06 –1.22 –1.16 –1.22 1.03 1.26 ubiquinone-binding protein QP-C Lamin PU00874 At5g15350 1.02 1.20 1.18 –1.06 1.01 1.07 Stellacyanin PU10974 At5g20230 1.01 –1.22 –1.23 –1.04 –1.06 –1.02 14 Functional Plant Biology Supplementary material

Appendix S6 continued Relative expression Leaves Stems Function Clone ID Gene ID 800/400 1200/400 1200/800 800/400 1200/400 1200/800 Copper binding protein-like, predicted PU07669 At5g26330 –1.03 1.14 1.17 –1.35 –1.08 1.24 GPI-anchored protein Copper binding protein-like, predicted PU06849 At5g26330 –1.08 –1.21 –1.11 –1.04 –1.03 1.01 GPI-anchored protein Copper binding protein-like, predicted PU01898 At5g26330 1.13 1.02 –1.11 –1.01 –1.13 –1.11 GPI-anchored protein Expressed protein PU11927 At5g26940 –1.03 –1.18 –1.14 –1.10 –1.13 –1.03 Expressed protein PU11208 At5g26940 –1.01 –1.09 –1.08 1.14 1.04 –1.10 Unknown protein (A_TM021B04.14) PU02512 At5g27280 –1.16 1.03 1.20 1.18 –1.04 –1.22 Thioredoxin PU05726 At5g39950 1.05 1.21 1.16 –1.31 –1.10 1.19 Thioredoxin PU10821 At5g39950 –1.09 1.05 1.15 –1.33 –1.13 1.18 Expressed protein PU11815 At5g40010 –1.17 –1.06 1.11 1.17 2.04 1.74 Expressed protein PU01068 At5g40010 –1.08 1.11 1.20 –1.34 1.06 1.42 Expressed protein PU09009 At5g49580 1.05 –1.00 –1.05 1.03 1.04 1.01 DNA repair protein-like PU12831 At5g50340 –1.06 –1.19 –1.13 1.03 1.22 1.19 Expressed protein PU00787 At5g52840 1.05 1.07 1.02 –1.06 –1.18 –1.11 Predicted GPI-anchored protein PU07706 At5g53870 –1.08 –1.11 –1.03 –1.31 1.01 1.32 Dihydropteroate synthase PU02143 At5g53870 1.14 –1.40 –1.59 –1.21 –1.06 1.14 Predicted GPI-anchored protein PU13084 At5g53870 1.01 1.09 1.08 –1.21 –1.10 1.10 Hypothetical 31.5 kDa protein PU13079 At5g53870 –1.14 –1.12 1.01 –1.52 –1.40 1.09 Expressed protein PU06536 At5g56090 –1.14 –1.05 1.09 1.02 1.17 1.14 Expressed protein PU13308 At5g56090 –1.04 1.03 1.06 –1.15 –1.21 –1.05 Expressed protein PU06222 At5g57815 1.07 –1.07 –1.14 1.15 –1.11 –1.28 Protein disulfide isomerase precursor-like PU01054 At5g60640 –1.11 –1.16 –1.05 1.10 1.15 1.05 Ferredoxin–NADP reductase, chloroplast PU09343 At5g66190 1.02 1.01 –1.01 1.29 1.76 1.36 precursor (EC 1.18.1.2) Chloroplast ferredoxin-NADP+ PU08844 At5g66190 1.02 –1.03 –1.05 1.24 1.51 1.22 oxidoreductase precursor(EC 1.18.1.2) Ferredoxin–NADP reductase, chloroplast PU09345 At5g66190 1.01 1.03 1.02 1.51 1.70 1.12 precursor (EC 1.18.1.2) Expressed protein PU02633 At5g66410 –1.07 –1.03 1.04 –1.45 –1.63 –1.13 Respiration AAA-metalloprotease FtsH PU04020 At1g07510 –1.04 –1.08 –1.04 –1.32 1.18 1.57 AAA-metalloprotease FtsH PU04056 At1g07510 1.11 1.00 –1.10 –1.16 1.28 1.49 Unknown protein (At1g07510) PU08044 At1g07510 1.10 –1.01 –1.11 –1.02 1.02 1.04 AAA-metalloprotease FtsH PU01723 At1g07510 1.05 1.03 –1.02 –1.07 –1.12 –1.05 Response regulator (two component PU01865 At1g74890 1.04 1.63 1.57 –1.21 1.08 1.31 phosphotransfer signalling) Expressed protein PU00494 At2g11000 –1.08 –1.00 1.08 1.07 –1.03 –1.10 Ethylene receptor PU09099 At3g23150 1.14 1.21 1.07 1.18 –1.06 –1.25 Ethylene receptor PU01195 At3g23150 –1.07 1.03 1.10 –1.28 –1.66 –1.29 Response regulator 5 PU06571 At3g57040 1.08 1.44 1.33 1.26 1.31 1.04 Response regulator PU04052 At3g57040 –1.09 –1.22 –1.11 –1.33 –2.07 –1.55 Predicted protein PU00870 At4g31920 –1.07 1.02 1.10 1.02 –1.09 –1.11 Expressed protein PU06238 At5g42870 –1.03 –1.03 1.00 –1.12 1.25 1.40 Phytocyanin/early nodulin-like protein PU12582 At5g57920 –1.58 –1.11 1.43 –1.59 –1.53 1.04 Fermentation FtsH-like protein Pftf precursor PU01020 At1g06430 –1.03 –1.04 –1.01 1.08 –1.23 –1.32 Chloroplast FtsH protease, putative PU03119 At1g50250 1.02 –1.01 –1.03 1.06 1.08 1.02 Chloroplast FtsH protease, putative PU10600 At1g50250 1.01 –1.13 –1.14 1.21 1.42 1.18 Chloroplast FtsH protease, putative PU05638 At1g50250 –1.03 –1.12 –1.09 1.08 1.11 1.03 FtsH like cell division protein PU06109 At1g79560 –1.14 –1.00 1.14 –1.03 –1.15 –1.12 Photosynthesis Photosystem I reaction centre subunit II, PU10316 At1g03130 –1.05 1.07 1.12 1.19 1.33 1.12 chloroplast precursor Supplementary material Functional Plant Biology 15

Appendix S6 continued Relative expression Leaves Stems Function Clone ID Gene ID 800/400 1200/400 1200/800 800/400 1200/400 1200/800 Photosystem I reaction centre subunit II, PU08452 At1g03130 –1.05 –1.03 1.02 1.21 1.32 1.10 chloroplast precursor Photosystem I reaction centre subunit II, PU10272 At1g03130 –1.01 1.05 1.07 1.14 1.20 1.05 chloroplast precursor Photosystem I reaction centre subunit II, PU08974 At1g03130 –1.12 1.00 1.12 1.32 1.21 –1.09 chloroplast precursor Photosystem I reaction centre subunit II, PU09496 At1g03130 1.14 1.01 –1.13 1.14 –1.10 –1.25 chloroplast precursor Expressed protein PU09899 At1g06150 1.03 1.05 1.02 1.02 –1.02 –1.04 Oxygen-evolving enhancer protein 2, PU08552 At1g06680 –1.06 –1.03 1.03 1.03 1.19 1.15 chloroplast [Precursor] Oxygen-evolving enhancer protein 2, PU01695 At1g06680 –1.11 –1.06 1.05 1.27 1.24 –1.02 chloroplast [Precursor] PsbQ domain protein family extrinsic pII PU09569 At1g14150 –1.10 –1.15 –1.05 1.25 1.11 –1.13 protein (Putative DNA-binding protein) PU08018 At1g15480 –1.16 1.10 1.28 –1.01 –1.21 –1.20 Chlorophyll a/b-binding protein CP24 PU12865 At1g15820 1.03 –1.08 –1.11 –1.30 1.07 1.39 Chlorophyll a/b-binding protein CP24 PU09300 At1g15820 1.08 1.17 1.08 1.01 1.21 1.20 Chlorophyll a/b-binding protein CP24 PU12094 At1g15820 –1.06 –1.19 –1.13 1.11 1.16 1.05 Chlorophyll a/b-binding protein CP24 PU10089 At1g15820 1.02 1.00 –1.02 1.03 1.04 1.01 Light-harvesting chlorophyll a/b binding PU08870 At1g19150 –1.08 –1.08 1.00 1.24 1.19 –1.04 protein Photosystem I subunit X precursor PU08421 At1g30380 1.04 –1.07 –1.11 1.38 1.49 1.08 Photosystem I subunit X precursor PU07325 At1g30380 –1.00 –1.07 –1.07 1.29 1.36 1.06 Photosystem I reaction centre subunit III PU01658 At1g31330 1.01 –1.04 –1.05 –1.07 1.05 1.13 Photosystem I reaction centre subunit III PU08515 At1g31330 1.01 1.01 –1.00 1.07 1.08 1.02 Pyruvate kinase isozyme G, chloroplast PU08246 At1g32440 1.09 –1.31 –1.44 –1.31 1.01 1.32 (EC 2.7.1.40) PSII K protein PU09437 At1g33000 1.12 –1.39 –1.55 1.03 –1.01 –1.04 Photosystem II 22 kDa protein, chloroplast PU11626 At1g44575 –1.08 –1.05 1.03 1.19 1.49 1.25 precursor (CP22) Photosystem II 22 kDa protein, chloroplast PU08493 At1g44575 –1.09 –1.05 1.04 –1.03 1.19 1.22 precursor (CP22) Photosystem I reaction center subunit V, PU08897 At1g55670 –1.07 –1.06 1.01 1.35 1.18 –1.15 chloroplast precursor PSI type III chlorophyll a/b-binding protein PU09129 At1g61520 –1.04 –1.02 1.02 1.63 1.53 –1.07 PSI type III chlorophyll a/b-binding protein PU11127 At1g61520 1.01 1.03 1.02 1.54 1.34 –1.15 PSI type III chlorophyll a/b-binding protein PU09641 At1g61520 1.03 1.02 –1.01 1.68 1.45 –1.16 PSI type III chlorophyll a/b-binding protein PU04287 At1g61520 1.05 –1.10 –1.16 1.57 1.35 –1.17 Protein psbY-1 (psbY-A1); Photosystem II PU09897 At1g67740 –1.07 –1.02 1.05 –1.02 1.16 1.19 protein psbY-2 (psbY-A2) Protein psbY-1 (psbY-A1); Photosystem II PU08423 At1g67740 –1.02 –1.14 –1.12 1.25 1.23 –1.02 protein psbY-2 (psbY-A2) Protein psbY-1 (psbY-A1); Photosystem II PU09945 At1g67740 –1.03 –1.16 –1.13 1.33 1.29 –1.03 protein psbY-2 (psbY-A2) Unknown protein PU09225 At1g77090 1.01 –1.11 –1.12 1.99 2.08 1.04 Photosystem II 10 kDa polypeptide, PU10192 At1g79040 –1.01 –1.00 1.01 –1.17 1.32 1.54 chloroplast precursor Photosystem II 10 kDa polypeptide, PU08701 At1g79040 –1.09 –1.02 1.07 –1.60 –1.08 1.47 chloroplast precursor Photosystem II 10 kDa polypeptide, PU09470 At1g79040 –1.10 1.05 1.16 –1.17 1.20 1.40 chloroplast precursor Photosystem II 10 kDa polypeptide, PU09038 At1g79040 –1.03 –1.00 1.03 –1.03 1.25 1.29 chloroplast precursor Photosystem II 10 kDa polypeptide, PU09360 At1g79040 –1.07 –1.02 1.05 –1.00 1.26 1.26 chloroplast precursor 16 Functional Plant Biology Supplementary material

Appendix S6 continued Relative expression Leaves Stems Function Clone ID Gene ID 800/400 1200/400 1200/800 800/400 1200/400 1200/800 Photosystem II 10 kDa polypeptide, PU02413 At1g79040 1.03 1.14 1.12 1.18 1.32 1.12 chloroplast precursor Photosystem II 10 kDa polypeptide, PU10701 At1g79040 –1.01 –1.01 –1.00 1.31 1.27 –1.03 chloroplast precursor Unknown protein (At1g80270; F5I6.2) PU13218 At1g80270 1.03 1.06 1.03 –1.19 –1.18 1.01 Unknown protein (At1g80270; F5I6.2) PU02399 At1g80270 –1.07 –1.14 –1.07 1.10 –1.05 –1.15 expressed protein PU08797 At2g04860 –1.01 –1.04 –1.03 –1.83 1.34 2.46 Light harvesting chlorophyll A/B binding PU09118 At2g05070 1.05 –1.20 –1.25 1.00 1.15 1.15 protein Light harvesting chlorophyll A/B binding PU10691 At2g05070 1.03 –1.04 –1.08 1.02 1.15 1.13 protein Light harvesting chlorophyll A/B binding PU08637 At2g05070 1.06 –1.13 –1.20 1.01 1.09 1.08 protein Light harvesting chlorophyll A/B binding PU09362 At2g05070 1.03 –1.16 –1.20 1.07 1.15 1.08 protein Light harvesting chlorophyll A/B binding PU09175 At2g05070 1.12 –1.17 –1.31 1.07 1.16 1.08 protein Light harvesting chlorophyll A/B binding PU01826 At2g05070 1.16 –1.19 –1.38 1.01 1.09 1.07 protein Photosystem II reaction center W protein, PU11769 At2g30570 –1.03 –1.08 –1.05 1.01 1.31 1.30 chloroplast precursor (PSII6.1 kDa protein) Photosystem II reaction center W protein, PU02972 At2g30570 1.01 –1.10 –1.10 –1.21 1.05 1.26 chloroplast precursor (PSII6.1 kDa protein) Photosystem II reaction center W protein, PU10194 At2g30570 –1.01 1.04 1.05 –1.04 –1.20 –1.15 chloroplast precursor (PSII6.1 kDa protein) Expressed protein PU12277 At2g34400 –1.02 –1.03 –1.01 1.09 –1.36 –1.48 Chlorophyll A/B binding protein precursor PU08388 At2g34430 –1.03 1.00 1.03 1.08 1.20 1.12 Chlorophyll A/B binding protein 3C, PU08563 At2g34430 1.02 –1.05 –1.07 1.04 1.13 1.08 chloroplast precursor (LHCII typeI CAB-3C) (LHCP) Chlorophyll A/B binding protein 3C, PU08740 At2g34430 –1.01 1.07 1.08 1.10 1.17 1.06 chloroplast precursor (LHCII typeI CAB-3C) (LHCP) Chlorophyll A/B binding protein precursor PU08473 At2g34430 1.04 –1.01 –1.06 1.14 1.19 1.04 Chlorophyll A/B binding protein 3C, PU08999 At2g34430 –1.01 –1.03 –1.02 1.16 1.19 1.03 chloroplast precursor (LHCII typeI CAB-3C) (LHCP) Chlorophyll A/B binding protein 3C, PU09860 At2g34430 1.01 1.05 1.04 1.12 1.15 1.03 chloroplast precursor (LHCII typeI CAB-3C) (LHCP) Chlorophyll A/B binding protein 3C, PU08697 At2g34430 –1.04 –1.02 1.01 1.21 1.21 –1.00 chloroplast precursor (LHCII typeI CAB-3C) (LHCP) Chlorophyll A/B binding protein 3C, PU08514 At2g34430 1.17 –1.09 –1.27 1.36 1.34 –1.01 chloroplast precursor (LHCII typeI CAB-3C) (LHCP) Chlorophyll A/B binding protein precursor PU01914 At2g34430 –1.03 1.03 1.06 1.15 1.11 –1.04 Chlorophyll A/B binding protein precursor PU04291 At2g34430 –1.06 –1.15 –1.09 –1.21 –1.30 –1.08 Chlorophyll A/B binding protein 3C, PU08688 At2g34430 –1.00 1.00 1.00 1.39 1.26 –1.10 chloroplast precursor (LHCII type I CAB-3C) (LHCP) Chlorophyll A/B binding protein 3C, PU08710 At2g34430 1.04 –1.07 –1.12 1.53 1.38 –1.10 chloroplast precursor (LHCII type I CAB-3C) (LHCP) Supplementary material Functional Plant Biology 17

Appendix S6 continued Relative expression Leaves Stems Function Clone ID Gene ID 800/400 1200/400 1200/800 800/400 1200/400 1200/800 Pyruvate kinase isozyme A, chloroplast PU06984 At3g22960 –1.05 –1.10 –1.05 1.12 1.12 –1.00 precursor (EC 2.7.1.40) Pyruvate kinase isozyme A, chloroplast PU06201 At3g22960 1.05 –1.17 –1.23 1.17 1.06 –1.10 precursor (EC 2.7.1.40) Pyruvate kinase isozyme A, chloroplast PU06014 At3g22960 –1.01 –1.04 –1.04 1.46 1.24 –1.18 precursor (EC 2.7.1.40) Hypothetical 27.6 kDa protein PU08505 At3g47470 –1.05 1.02 1.08 1.00 1.38 1.38 Hypothetical 27.6 kDa protein PU00355 At3g47470 –1.14 1.00 1.14 1.31 1.17 –1.11 Hypothetical 27.6 kDa protein PU00827 At3g47470 –1.11 1.00 1.11 1.42 1.22 –1.17 Hypothetical 27.6 kDa protein PU08457 At3g47470 –1.08 1.08 1.17 1.54 1.26 –1.22 Hypothetical 27.6 kDa protein PU08568 At3g47470 –1.16 –1.06 1.10 1.63 1.31 –1.25 Oxygen evolving enhancer protein 1 precursor PU08491 At3g50820 –1.05 –1.04 1.01 1.06 1.15 1.09 Oxygen evolving enhancer protein 1 precursor PU00411 At3g50820 –1.10 –1.05 1.04 1.20 1.25 1.05 Oxygen evolving enhancer protein 1 precursor PU09125 At3g50820 –1.02 –1.08 –1.06 1.26 1.25 –1.01 Oxygen evolving enhancer protein 1 precursor PU04452 At3g50820 –1.02 –1.03 –1.01 1.32 1.24 –1.06 Pyruvate kinase-like protein PU03877 At3g52990 1.01 1.14 1.12 –1.20 –1.11 1.08 Pyruvate kinase-like protein PU01941 At3g52990 1.17 –1.02 –1.20 –1.12 –1.04 1.08 Pyruvate kinase-like protein PU12762 At3g52990 1.07 1.16 1.08 –1.03 1.03 1.06 Pyruvate kinase-like protein PU13112 At3g52990 –1.32 –1.31 1.01 –1.15 –1.10 1.05 Pyruvate kinase-like protein PU08136 At3g52990 1.16 –1.00 –1.17 1.05 –1.05 –1.11 Pyruvate kinase-like protein PU04889 At3g52990 1.02 1.02 –1.00 1.01 –1.17 –1.17 Photosystem I light-harvesting chlorophyll PU08680 At3g54890 –1.03 1.04 1.07 1.23 1.17 –1.05 a/b-binding protein Photosystem I light-harvesting chlorophyll PU09731 At3g54890 –1.04 1.04 1.09 –1.04 –1.12 –1.07 a/b-binding protein Photosystem I light-harvesting chlorophyll PU08784 At3g54890 –1.04 1.06 1.10 1.03 –1.08 –1.11 a/b-binding protein Chlorophyll A/B binding protein 7, PU09715 At3g61470 –1.01 1.03 1.03 1.37 1.66 1.21 chloroplast precursor (LHCI type IICAB-7) Chlorophyll A/B binding protein 7, PU02558 At3g61470 –1.02 –1.01 1.01 1.30 1.35 1.04 chloroplast precursor (LHCI type IICAB-7) Chlorophyll a/b-binding protein-like PU09440 At4g10340 1.00 –1.13 –1.13 –1.56 –1.31 1.19 Chlorophyll a/b-binding protein-like PU09468 At4g10340 –1.03 –1.09 –1.05 1.00 1.09 1.08 Chlorophyll a/b-binding protein-like PU08995 At4g10340 1.00 –1.03 –1.03 –1.02 –1.00 1.02 Chlorophyll a/b-binding protein-like PU02643 At4g10340 –1.02 –1.10 –1.08 1.14 1.15 1.01 Chlorophyll a/b-binding protein-like PU09649 At4g10340 –1.05 –1.05 –1.01 1.08 1.06 –1.02 Chlorophyll a/b-binding protein-like PU08475 At4g10340 –1.00 1.02 1.02 1.16 1.05 –1.11 Chlorophyll a/b-binding protein-like PU08883 At4g10340 –1.12 –1.11 1.00 1.17 1.01 –1.16 Probable photosystem I chain XI precursor PU09380 At4g12800 –1.01 1.03 1.05 1.02 1.12 1.10 Probable photosystem I chain XI precursor PU10462 At4g12800 –1.06 1.06 1.12 1.09 1.04 –1.05 Probable photosystem I chain XI precursor PU10414 At4g12800 –1.02 1.05 1.07 1.09 –1.06 –1.16 Oxygen-evolving complex 25.6 kD protein, PU09143 At4g15510 –1.14 –1.13 1.01 –1.18 1.01 1.18 chloroplast precursor Oxygen-evolving complex 25.6 kD protein, PU09145 At4g15510 –1.11 1.06 1.18 –1.22 –1.25 –1.02 chloroplast precursor Expressed protein PU10952 At4g15510 1.03 –1.16 –1.19 1.11 1.00 –1.10 Expressed protein PU10746 At4g17620 –1.13 –1.11 1.02 –1.07 1.22 1.31 Brain protein 44 PU10976 At4g22310 –1.08 –1.11 –1.03 1.19 1.31 1.10 Expressed protein PU04732 At4g22310 –1.06 1.04 1.11 –1.01 –1.11 –1.10 Expressed protein PU09759 At4g25270 –1.11 1.01 1.13 –1.02 1.03 1.05 Y20 protein PU09568 At4g27270 1.04 –1.00 –1.04 –1.11 1.20 1.33 Y20 protein PU11588 At4g27270 –1.17 –1.04 1.12 –1.31 –1.52 –1.17 Photosystem II protein W-like PU10357 At4g28660 1.05 –1.15 –1.21 1.19 1.95 1.63 H+-transporting ATP synthase chain 9-like PU11501 At4g32260 –1.11 –1.12 –1.01 1.07 1.67 1.56 protein 18 Functional Plant Biology Supplementary material

Appendix S6 continued Relative expression Leaves Stems Function Clone ID Gene ID 800/400 1200/400 1200/800 800/400 1200/400 1200/800 H+-transporting ATP synthase chain 9-like PU12414 At4g32260 –1.08 –1.15 –1.06 –1.02 –1.10 –1.09 protein H+-transporting ATP synthase chain 9-like PU09475 At4g32260 –1.06 –1.14 –1.08 1.07 –1.02 –1.09 protein H+-transporting ATP synthase chain 9-like PU10343 At4g32260 –1.04 –1.17 –1.12 1.34 1.05 –1.28 protein Minor allergen PU03958 At4g36750 1.42 1.34 –1.06 1.60 2.01 1.25 Minor allergen PU07798 At4g36750 –1.00 1.12 1.12 1.06 –1.05 –1.11 Minor allergen PU08100 At4g36750 1.02 1.12 1.09 –1.07 –1.20 –1.12 Chlorophyll a/b-binding protein CP29 PU06076 At5g01530 –1.10 1.05 1.16 1.03 –1.06 –1.09 Chlorophyll a/b-binding protein CP30 PU09088 At5g01530 –1.09 1.12 1.23 1.25 1.13 –1.11 Chlorophyll a/b-binding protein CP31 PU09368 At5g01530 –1.10 1.04 1.15 1.19 1.05 –1.14 One helix protein (OHP) PU11714 At5g02120 –1.19 –1.12 1.06 1.37 1.24 –1.11 Pyruvate kinase, cytosolic isozyme PU06775 At5g08570 1.08 –1.00 –1.08 –1.13 1.07 1.21 (EC 2.7.1.40) Pyruvate kinase, cytosolic isozyme PU05377 At5g08570 1.03 –1.10 –1.13 –1.13 1.02 1.14 (EC 2.7.1.40) Pyruvate kinase, cytosolic isozyme PU03187 At5g08570 1.05 –1.03 –1.08 1.23 1.29 1.05 (EC 2.7.1.40) Pyruvate kinase, cytosolic isozyme PU10936 At5g08570 1.07 –1.04 –1.12 1.09 1.04 –1.04 (EC 2.7.1.40) Pyruvate kinase, cytosolic isozyme PU06747 At5g08570 1.03 –1.09 –1.12 1.12 1.05 –1.07 (EC 2.7.1.40) Oxygen-evolving complex related protein PU08709 At5g11450 –1.16 –1.09 1.06 1.19 1.21 1.01 23 kDa polypeptide Expressed protein PU02075 At5g20090 –1.01 –1.12 –1.12 –1.14 –1.16 –1.01 LHCII type III chlorophyll a/b-binding protein PU03295 At5g54270 –1.08 –1.03 1.06 –1.26 1.34 1.69 LHCII type III chlorophyll a/b-binding protein PU08450 At5g54270 1.10 –1.02 –1.12 1.15 1.28 1.11 LHCII type III chlorophyll a/b-binding protein PU00298 At5g54270 1.17 –1.02 –1.20 1.29 1.40 1.09 1,4-benzoquinone reductase-like; Trp PU02254 At5g54500 1.14 1.28 1.11 –1.11 1.20 1.32 repressor binding protein-like Hypothetical 21.7 kDa protein PU01283 At5g54500 1.03 –1.10 –1.13 1.23 1.55 1.26 1,4-benzoquinone reductase-like; Trp PU01800 At5g54500 1.05 1.03 –1.03 1.10 1.35 1.23 repressor binding protein-like Hypothetical 21.7 kDa protein PU01588 At5g54500 –1.05 1.04 1.09 –1.07 –1.07 1.00 Hypothetical 21.7 kDa protein PU11705 At5g54500 –1.01 –1.08 –1.08 –1.33 –1.50 –1.13 Pyruvate kinase PU05921 At5g56350 –1.13 –1.03 1.10 –1.25 1.18 1.46 Pyruvate kinase PU01181 At5g56350 1.00 –1.11 –1.12 –1.38 –1.04 1.32 Pyruvate kinase PU11807 At5g56350 1.03 –1.05 –1.08 –1.21 –1.19 1.01 Photosystem I reaction centre subunit psaN PU09419 At5g64040 1.01 –1.14 –1.14 1.31 1.18 –1.11 precursor Photosystem I reaction centre subunit psaN PU10257 At5g64040 1.10 –1.16 –1.27 1.39 1.20 –1.16 precursor Rubisco and Calvin cycle Sucrose-phosphate synthase, putative PU03569 At1g04920 1.02 1.01 –1.01 –1.20 –1.17 1.03 Glyceraldehyde 3-phosphate dehydrogenase PU08978 At1g12900 1.07 –1.07 –1.15 –1.44 –1.12 1.29 B, chloroplast UDP-glycosyltransferase family PU08910 At1g22360 1.07 1.24 1.16 –1.12 –1.09 1.03 Phosphoglucomutase, cytoplasmic PU13421 At1g23190 1.04 –1.02 –1.06 –1.05 1.02 1.07 (EC 5.4.2.2) Phosphoglucomutase, cytoplasmic PU00915 At1g23190 1.06 1.01 –1.05 –1.01 1.01 1.03 (EC 5.4.2.2) Phosphoglucomutase, cytoplasmic PU06231 At1g23190 1.10 1.01 –1.09 1.12 1.15 1.03 (EC 5.4.2.2) Phosphoribulokinase, chloroplast precursor PU11066 At1g32060 –1.04 –1.08 –1.04 1.29 1.11 –1.16 (EC 2.7.1.19) Supplementary material Functional Plant Biology 19

Appendix S6 continued Relative expression Leaves Stems Function Clone ID Gene ID 800/400 1200/400 1200/800 800/400 1200/400 1200/800 POSSIBLY putative PU08785 At1g42970 1.01 1.04 1.03 1.12 1.11 –1.01 glyceraldehyde-3-phosphate dehydrogenase (At1g42970) D-ribulose-5-phosphate 3-epimerase PU02541 At1g63290 –1.00 1.03 1.04 –1.11 –1.13 –1.01 (EC 5.1.3.1) Ribulose bisphosphate carboxylase small PU09239 At1g67090 –1.02 –1.02 1.01 1.11 1.41 1.27 chain 3, chloroplast precursor (EC 4.1.1.39) Ribulose bisphosphate carboxylase small PU12328 At1g67090 –1.00 1.06 1.07 1.21 1.50 1.25 chain 3, chloroplast precursor (EC 4.1.1.39) Ribulose bisphosphate carboxylase small PU08898 At1g67090 1.04 1.02 –1.02 1.10 1.33 1.21 chain 3, chloroplast precursor (EC 4.1.1.39) Ribulose bisphosphate carboxylase small PU09041 At1g67090 1.04 –1.01 –1.05 1.19 1.44 1.21 chain 3, chloroplast precursor (EC 4.1.1.39) Ribulose bisphosphate carboxylase small PU08803 At1g67090 1.03 –1.00 –1.03 1.46 1.76 1.21 chain 3, chloroplast precursor (EC 4.1.1.39) Ribulose bisphosphate carboxylase small PU06295 At1g67090 1.01 –1.02 –1.03 1.19 1.43 1.20 chain 3, chloroplast precursor (EC 4.1.1.39) Ribulose bisphosphate carboxylase small PU09462 At1g67090 1.00 1.03 1.03 1.14 1.35 1.19 chain 3, chloroplast precursor (EC 4.1.1.39) Ribulose bisphosphate carboxylase small PU09374 At1g67090 –1.03 1.05 1.08 1.18 1.37 1.16 chain 3, chloroplast precursor (EC 4.1.1.39) Ribulose bisphosphate carboxylase small PU09089 At1g67090 1.03 1.03 1.01 1.06 1.22 1.15 chain 3, chloroplast precursor (EC 4.1.1.39) Ribulose bisphosphate carboxylase small PU08633 At1g67090 –1.00 1.02 1.02 1.21 1.39 1.15 chain 3, chloroplast precursor (EC 4.1.1.39) Ribulose bisphosphate carboxylase small PU09264 At1g67090 1.02 1.02 –1.00 1.13 1.29 1.14 chain 3, chloroplast precursor (EC 4.1.1.39) Ribulose bisphosphate carboxylase small PU08825 At1g67090 1.02 1.04 1.02 1.24 1.40 1.13 chain 3, chloroplast precursor (EC 4.1.1.39) Ribulose bisphosphate carboxylase small PU08913 At1g67090 1.01 1.09 1.08 1.15 1.29 1.12 chain 3, chloroplast precursor (EC 4.1.1.39) Ribulose bisphosphate carboxylase small PU09043 At1g67090 –1.00 1.07 1.08 1.22 1.36 1.12 chain 3, chloroplast precursor (EC 4.1.1.39) Ribulose bisphosphate carboxylase small PU10298 At1g67090 1.01 1.03 1.02 1.23 1.38 1.12 chain 3, chloroplast precursor (EC 4.1.1.39) Ribulose bisphosphate carboxylase small PU12369 At1g67090 –1.05 –1.01 1.04 1.01 1.13 1.12 chain 3, chloroplast precursor (EC 4.1.1.39) Ribulose bisphosphate carboxylase small PU09553 At1g67090 1.02 1.02 1.00 1.16 1.27 1.10 chain 3, chloroplast precursor (EC 4.1.1.39) 20 Functional Plant Biology Supplementary material

Appendix S6 continued Relative expression Leaves Stems Function Clone ID Gene ID 800/400 1200/400 1200/800 800/400 1200/400 1200/800 Ribulose bisphosphate carboxylase small PU08428 At1g67090 1.01 1.08 1.07 1.40 1.53 1.10 chain 3, chloroplast precursor (EC 4.1.1.39) Ribulose bisphosphate carboxylase small PU08539 At1g67090 1.02 –1.03 –1.05 1.33 1.45 1.09 chain 3, chloroplast precursor (EC 4.1.1.39) Ribulose bisphosphate carboxylase small PU10119 At1g67090 1.05 1.04 –1.01 1.31 1.42 1.09 chain 3, chloroplast precursor (EC 4.1.1.39) Ribulose bisphosphate carboxylase small PU09232 At1g67090 1.05 1.05 –1.00 1.41 1.50 1.07 chain 3, chloroplast precursor (EC 4.1.1.39) Ribulose bisphosphate carboxylase small PU09363 At1g67090 1.02 1.03 1.01 1.20 1.28 1.07 chain 3, chloroplast precursor (EC 4.1.1.39) Ribulose bisphosphate carboxylase small PU08779 At1g67090 1.05 –1.24 –1.31 1.11 1.18 1.06 chain 3, chloroplast precursor (EC 4.1.1.39) Ribulose bisphosphate carboxylase small PU08492 At1g67090 1.01 –1.04 –1.05 1.22 1.29 1.05 chain 3, chloroplast precursor (EC 4.1.1.39) Ribulose bisphosphate carboxylase small PU10250 At1g67090 1.02 1.07 1.05 1.31 1.38 1.05 chain 3, chloroplast precursor (EC 4.1.1.39) Ribulose bisphosphate carboxylase small PU11603 At1g67090 1.03 1.01 –1.02 1.22 1.27 1.04 chain 3, chloroplast precursor (EC 4.1.1.39) Ribulose bisphosphate carboxylase small PU10817 At1g67090 1.04 –1.08 –1.12 –1.15 –1.11 1.04 chain 3, chloroplast precursor (EC 4.1.1.39) Ribulose bisphosphate carboxylase small PU09012 At1g67090 –1.07 1.04 1.11 1.16 1.20 1.03 chain 3, chloroplast precursor (EC 4.1.1.39) Ribulose bisphosphate carboxylase small PU08560 At1g67090 1.01 1.01 –1.00 1.22 1.24 1.02 chain 3, chloroplast precursor(EC 4.1.1.39) Ribulose bisphosphate carboxylase small PU10714 At1g67090 1.02 –1.03 –1.05 1.26 1.26 1.00 chain 3, chloroplast precursor (EC 4.1.1.39) Ribulose bisphosphate carboxylase small PU11281 At1g67090 1.02 –1.01 –1.03 1.28 1.27 –1.01 chain 3, chloroplast precursor (EC 4.1.1.39) Ribulose bisphosphate carboxylase small PU03769 At1g67090 1.02 –1.07 –1.10 1.27 1.14 –1.12 chain 3, chloroplast precursor (EC 4.1.1.39) Ribulose bisphosphate carboxylase small PU08993 At1g67090 1.03 1.03 –1.01 1.04 –1.08 –1.12 chain 3, chloroplast precursor (EC 4.1.1.39) Ribulose bisphosphate carboxylase small PU08765 At1g67090 –1.03 1.03 1.06 1.42 1.14 –1.24 chain 3, chloroplast precursor (EC 4.1.1.39) similar to glucoronosyl transferase-like PU10937 At1g78270 1.14 –1.01 –1.15 –1.51 –1.37 1.10 protein Triosephosphate isomerase, chloroplast PU07742 At2g21170 1.00 1.01 1.01 –1.09 1.11 1.20 precursor (EC 5.3.1.1) Triosephosphate isomerase, chloroplast PU05808 At2g21170 –1.05 –1.02 1.03 –1.13 1.06 1.20 precursor (EC 5.3.1.1) Supplementary material Functional Plant Biology 21

Appendix S6 continued Relative expression Leaves Stems Function Clone ID Gene ID 800/400 1200/400 1200/800 800/400 1200/400 1200/800 Triosephosphate isomerase, chloroplast PU06653 At2g21170 1.01 –1.01 –1.02 –1.04 1.03 1.08 precursor (EC 5.3.1.1) (Glyceraldehyde-3-phosphate dehydrogenase PU08451 At2g24270 1.17 –1.22 –1.42 –1.08 1.51 1.63 [NADP+]) (Triosephosphatedehydrogenase) (Glyceraldehyde-3-phosphate dehydrogenase PU09033 At2g24270 1.22 –1.20 –1.47 1.06 1.57 1.48 [NADP+]) (Triosephosphatedehydrogenase) (Glyceraldehyde-3-phosphate dehydrogenase PU09037 At2g24270 1.26 –1.19 –1.50 1.23 1.51 1.23 [NADP+]) (Triosephosphatedehydrogenase) Rubisco activase PU11445 At2g39730 1.17 1.00 –1.16 1.21 1.60 1.33 Rubisco activase PU11249 At2g39730 1.05 –1.06 –1.11 –1.04 1.06 1.10 Rubisco activase PU08719 At2g39730 1.04 –1.05 –1.10 1.68 1.81 1.08 Transketolase, chloroplast (EC 2.2.1.1) PU07838 At2g45290 1.08 –1.18 –1.28 –1.04 –1.12 –1.08 Transketolase, chloroplast (EC 2.2.1.1) PU02587 At2g45290 1.09 –1.14 –1.24 1.12 –1.03 –1.16 Beta-amylase PU13041 At2g45880 –1.09 –1.47 –1.34 –1.46 –1.18 1.24 Sucrose synthase PU02568 At3g43190 1.17 1.20 1.03 1.49 1.40 –1.07 Sucrose synthase PU06267 At3g43190 1.04 –1.03 –1.07 1.52 1.15 –1.32 Sucrose synthase PU07712 At3g43190 1.14 1.21 1.06 1.22 –1.09 –1.33 Sucrose synthase PU07980 At3g43190 1.13 –1.10 –1.25 1.74 1.25 –1.39 Sucrose synthase PU07545 At3g43190 1.21 –1.28 –1.54 1.82 1.31 –1.39 Sucrose synthase PU00401 At3g43190 1.09 –1.05 –1.14 2.11 1.41 –1.50 Sucrose synthase PU01211 At3g43190 1.08 –1.37 –1.47 1.47 –1.07 –1.57 Sedoheptulose-1,7-bisphosphatase, PU09289 At3g55800 1.05 –1.20 –1.26 –1.24 1.28 1.58 chloroplast precursor (EC 3.1.3.37) Sedoheptulose-1,7-bisphosphatase, PU10917 At3g55800 1.06 –1.26 –1.33 1.08 1.47 1.36 chloroplast precursor (EC 3.1.3.37) Sedoheptulose-1,7-bisphosphatase, PU01501 At3g55800 1.00 –1.20 –1.21 –1.01 –1.04 –1.02 chloroplast precursor (EC 3.1.3.37) Sedoheptulose-1,7-bisphosphatase, PU09166 At3g55800 –1.02 –1.13 –1.11 1.24 1.12 –1.11 chloroplast precursor (EC 3.1.3.37) Sucrose synthase PU03976 At4g02280 –1.15 –1.07 1.08 –1.38 1.05 1.45 Sucrose synthase PU01379 At4g02280 –1.00 –1.10 –1.09 1.03 1.28 1.24 Sucrose synthase PU12928 At4g02280 –1.20 –1.06 1.13 –1.02 1.17 1.19 Sucrose synthase PU12930 At4g02280 –1.06 1.09 1.16 1.03 1.20 1.16 Sucrose synthase PU09676 At4g02280 –1.06 1.01 1.07 1.44 1.33 –1.08 Sucrose-phosphate synthase-like protein PU09723 At4g10120 1.11 1.02 –1.09 –1.47 –1.38 1.07 Beta-amylase (EC 3.2.1.2) PU03585 At4g15210 –1.34 1.10 1.48 –1.62 1.11 1.81 Beta-amylase (EC 3.2.1.2) PU03653 At4g15210 –1.37 –1.01 1.35 –1.69 –1.01 1.66 Beta-amylase PCT-BMYI (EC 3.2.1.2) PU09978 At4g17090 –1.17 –1.03 1.14 –1.14 –1.13 1.00 Starch branching enzyme I precursor PU06428 At5g03650 –1.05 1.06 1.11 1.10 1.39 1.27 Starch branching enzyme I precursor PU08471 At5g03650 –1.01 –1.04 –1.04 1.09 1.28 1.18 Hypothetical 41.9 kDa protein PU05543 At5g13420 1.09 1.24 1.14 –1.19 –1.13 1.05 Hypothetical 41.9 kDa protein PU07440 At5g13420 1.03 1.19 1.15 –1.08 –1.15 –1.07 Beta-amylase-like proten PU04549 At5g18670 1.05 1.11 1.06 1.81 1.89 1.05 Sucrose-phosphate synthase 1 (EC 2.4.1.14) PU09622 At5g20280 1.07 1.06 –1.02 –1.08 1.32 1.42 Sucrose-phosphate synthase 1 (EC 2.4.1.14) PU07499 At5g20280 –1.01 –1.03 –1.02 1.07 1.17 1.10 Sucrose synthase PU07221 At5g20830 –1.02 1.09 1.11 –1.33 –1.14 1.17 Sucrose synthase PU07957 At5g20830 1.11 –1.23 –1.37 1.66 1.33 –1.25 Phosphoglucomutase PU02739 At5g51820 –1.12 –1.14 –1.01 1.51 1.56 1.03 Phosphoglucomutase PU04213 At5g51820 –1.11 –1.08 1.03 1.20 1.05 –1.15 Nibulose-5-phosphate-3-epimerase PU06579 At5g61410 –1.10 –1.09 1.01 –1.13 1.01 1.14 22 Functional Plant Biology Supplementary material

Appendix S6 continued Relative expression Leaves Stems Function Clone ID Gene ID 800/400 1200/400 1200/800 800/400 1200/400 1200/800 Photorespiration Aminomethyltransferase, mitochondrial PU09074 At1g11860 1.01 –1.13 –1.14 1.23 1.26 1.02 precursor (EC 2.1.2.10) Aminomethyltransferase, mitochondrial PU07242 At1g11860 1.06 –1.09 –1.15 1.30 1.20 –1.09 precursor (EC 2.1.2.10) Catalase isozyme 1 (EC 1.11.1.6) PU09186 At1g20630 –1.04 –1.16 –1.11 –1.03 1.02 1.06 Hydroxymethyltransferase like protein PU04914 At1g36370 1.04 1.17 1.13 –1.39 –1.24 1.11 Hydroxypyruvate reductase (EC 1.1.1.29) PU10880 At1g68010 1.05 1.01 –1.04 1.04 1.38 1.32 Glycine decarboxylase complex H-protein PU05496 At2g35120 –1.07 –1.03 1.04 –1.20 –1.07 1.12 Glycine decarboxylase complex H-protein PU01744 At2g35120 –1.23 –1.20 1.02 –1.11 –1.07 1.03 Glycolate oxidase, putative PU05752 At3g14150 1.06 1.23 1.17 1.21 1.11 –1.08 Glycolate oxidase (EC 1.1.3.15) PU08652 At3g14415 1.08 –1.08 –1.17 1.13 1.07 –1.06 Glutamine synthetase (EC 6.3.1.2) PU11411 At3g17820 1.07 –1.02 –1.08 –1.31 1.45 1.90 Hydroxymethyltransferase PU00316 At4g13930 1.09 1.01 –1.09 –1.26 –1.07 1.18 Hydroxymethyltransferase PU02529 At4g13930 1.15 –1.04 –1.20 1.21 1.40 1.16 Hydroxymethyltransferase PU02209 At4g13930 1.16 –1.01 –1.16 1.20 1.22 1.02 Hydroxymethyltransferase PU06217 At4g13930 1.19 –1.01 –1.21 1.13 –1.22 –1.37 Glycine hydroxymethyltransferase (EC PU03587 At4g32520 –1.08 –1.06 1.02 –1.16 –1.18 –1.02 2.1.2.1)-like protein Catalase isozyme 1 (EC 1.11.1.6) PU11606 At4g35090 1.06 1.03 –1.03 1.13 1.24 1.11 Catalase isozyme 1 (EC 1.11.1.6) PU02760 At4g35090 1.01 1.13 1.11 –1.05 1.03 1.07 Serine hydroxymethyltransferase, PU07376 At4g37930 1.09 –1.07 –1.16 1.02 1.14 1.11 mitochondrial precursor (EC 2.1.2.1) Ferredoxin-dependent glutamate synthase, PU09069 At5g04140 1.04 1.02 –1.02 1.04 –1.05 –1.09 chloroplast (EC 1.4.7.1) Glutamine synthetase precursor (EC 6.3.1.2) PU12880 At5g35630 1.02 –1.13 –1.15 –1.50 –1.23 1.22 Glutamine synthetase precursor (EC 6.3.1.2) PU06395 At5g35630 –1.16 –1.07 1.08 1.32 –1.12 –1.48 Glutamine synthetase nodule isozyme PU02286 At5g37600 1.04 1.17 1.12 –1.06 1.33 1.41 (EC 6.3.1.2) Glutamine synthetase nodule isozyme PU02929 At5g37600 1.11 1.19 1.08 1.18 1.43 1.22 (EC 6.3.1.2) Glutamine synthetase nodule isozyme PU06913 At5g37600 1.02 1.19 1.16 –1.16 –1.00 1.16 (EC 6.3.1.2) Glutamine synthetase nodule isozyme PU00010 At5g37600 1.24 1.32 1.06 1.09 1.18 1.08 (EC 6.3.1.2) Glutamine synthetase nodule isozyme PU08292 At5g37600 1.12 1.27 1.13 1.02 –1.03 –1.05 (EC 6.3.1.2) Glutamine synthetase nodule isozyme PU02327 At5g37600 1.03 1.12 1.09 1.36 1.24 –1.09 (EC 6.3.1.2) Glutamine synthetase nodule isozyme PU04179 At5g37600 1.02 1.12 1.10 1.22 1.09 –1.12 (EC 6.3.1.2) Glutamine synthetase nodule isozyme PU01775 At5g37600 1.17 1.09 –1.07 –1.11 –1.36 –1.22 (EC 6.3.1.2) Glutamine synthetase nodule isozyme PU06292 At5g37600 1.17 1.22 1.04 1.63 1.23 –1.32 (EC 6.3.1.2) Other energy activities Cysteine proteinase PU07286 At1g20850 –1.11 –1.09 1.02 –1.52 –1.08 1.41 Cysteine proteinase PU02345 At1g20850 1.02 1.48 1.45 –1.08 1.03 1.11 Thiol protease PU04803 At1g20850 1.10 –1.04 –1.14 1.28 –1.12 –1.43 Expressed protein PU07961 At1g58110 1.04 1.10 1.06 –1.12 –1.06 1.06 Expressed protein PU07332 At1g63300 –1.05 1.07 1.13 –1.05 –1.19 –1.13 Expressed protein PU04956 At1g63300 1.09 –1.09 –1.18 –1.18 –1.42 –1.20 Membrane trafficking factor PU02895 At4g04210 –1.08 –1.10 –1.01 1.05 1.03 –1.03 ATP synthase delta chain, chloroplast PU12504 At4g13340 1.04 –1.03 –1.07 1.15 1.19 1.03 precursor (EC 3.6.3.14) Supplementary material Functional Plant Biology 23

Appendix S6 continued

Relative expression Leaves Stems Function Clone ID Gene ID 800/400 1200/400 1200/800 800/400 1200/400 1200/800 Endoplasmin homolog precursor PU04411 At4g24190 1.18 1.72 1.46 1.28 1.27 –1.01 (GRP94 homolog) Endoplasmin homolog precursor PU12289 At4g24190 1.16 1.62 1.40 1.23 1.15 –1.07 (GRP94 homolog) Endoplasmin homolog precursor PU01841 At4g24190 1.08 1.59 1.47 1.23 1.08 –1.14 (GRP94 homolog) Papain-like cysteine proteinase isoform I PU07684 At4g39090 1.09 1.23 1.13 –1.23 –1.09 1.14 Papain-like cysteine proteinase isoform I PU02705 At4g39090 1.04 1.07 1.02 1.07 1.14 1.07 Papain-like cysteine proteinase isoform I PU06015 At4g39090 1.03 1.13 1.10 –1.23 –1.35 –1.10 Papain-like cysteine proteinase isoform I PU04135 At4g39090 1.11 1.11 –1.00 –1.15 –1.44 –1.26 Papain-like cysteine proteinase isoform I PU07717 At4g39090 1.00 1.17 1.17 –1.10 –1.39 –1.27 ATP synthase beta chain, mitochondrial PU04562 At5g08670 1.01 –1.01 –1.03 –1.24 1.05 1.29 precursor (EC 3.6.3.14) ATP synthase beta chain, mitochondrial PU03047 At5g08670 –1.29 1.23 1.59 –1.02 1.13 1.14 precursor (EC 3.6.3.14) ATP synthase beta chain, mitochondrial PU00228 At5g08670 1.08 –1.00 –1.08 1.06 –1.14 –1.21 precursor (EC 3.6.3.14) ATP synthase beta chain, mitochondrial PU07285 At5g08670 1.14 1.11 –1.03 –1.07 –1.35 –1.26 precursor (EC 3.6.3.14) 12-oxophytodienoate reductase 3 PU05322 At5g55230 1.02 –1.14 –1.17 –1.34 –1.01 1.33 (EC 1.3.1.42) 12-oxophytodienoate reductase 3 PU04474 At5g55230 1.05 –1.10 –1.15 1.05 1.29 1.23 (EC 1.3.1.42) DnaJ-like protein PU02939 At5g55230 1.02 1.15 1.13 –1.02 –1.06 –1.03 12-oxophytodienoate reductase 3 PU12490 At5g55230 –1.04 1.02 1.06 1.17 1.02 –1.15 (EC 1.3.1.42) Heat shock protein PU05022 At5g56000 1.28 1.07 –1.19 2.50 2.58 1.03

24 Functional Plant Biology Supplementary material

Leaves Stems & pelargonidin & pelargonidin cyanidin, rutin & 3-metoxyluteolin 3-methoxyapigenin delphinidin cyanidin, rutin & 3-methoxyapigenin delphinidin 3-metoxyluteolin DFR DFR DFR DFR DFR DFR , from left to right, changes dihydromyricetin dihydromyricetin F3• 5• H F3• 5• H F3• 5• H F3• 5• H F3H F3H L, 4-coumarate-CoA C4H, trans-cinnamate ligase; n 3-dioxygenase; F3´H, flavonoid 3´-monooxygenase; F3´H, flavonoid n 3-dioxygenase; F3• H F3• H The coloured squares represent squares coloured The F3H F3H n fold change. n fold F3• 5• H F3• 5• H dihydrokaempferol dihydrokaempferol pentahydroxyflavone pentahydroxyflavone eridictyol dihydroquercetin eridictyol dihydroquercetin F3• H F3• H F3H F3H F3• 5• H F3• 5• H cts expression ratios i ratios cts expression naringenin erol 4-reductase; F3H, naringeni F3H, erol 4-reductase; naringenin in leaves and stems of poplar. and stems of poplar. in leaves CHI CHI average of all samples from all treatments. 4C from all treatments. samples of all average Appendix S7 Appendix scale on the left depi the scale on in silico naringenin-chalcone naringenin-chalcone CHS CHS one synthase; DFR, dihydrokaempf one synthase; DFR, -coumarate-CoA -coumarate-CoA p p respectively, relative to the relative respectively, 2 4CL 4CL CO –1 -coumarate -coumarate p p C4H C4H ] on the expression of genes of the flavonol biosynthesis pathway pathway biosynthesis flavonol the of of genes expression the ] on PAL, phenylalanine ammonia-lyase. The colour The colour ammonia-lyase. phenylalanine PAL, 2 cinnamate cinnamate PAL PAL L-phenylalanine L-phenylalanine

2.0 1.0 -2.0 Relative gene expression (fold change) (fold expression gene Relative F3´5´H, flavonoid 3´,5´ hydroxylase; 3´,5´ flavonoid F3´5´H, 4-monooxygenase; CHI, chalcone isomerase; CHS, naringenin-chalc chalcone isomerase; CHS, CHI, 4-monooxygenase; in gene expression at 400, 800 and 1200 mol 800 and 1200 µmol at 400, in gene expression Model of the effects of elevated [CO of elevated of the effects Model